Boutros - Ahr-null and Wild-type Mice - TCDD - Liver/Kidney Microarray
Warren Sink
12/10/2021
1 Differentially regulated genes by the AhR using Ahr-null mice and the AhR-selective ligand, TCDD
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This document serves as a record for the reprisal of the kidney and liver cDNA microarrays from the publication Dioxin-Dependent and Dioxin-Independent Gene Batteries: Comparison of Liver and Kidney in AHR-Null Mice. Boutros et al. evaluated AhR-regulated gene expression with 15-week-old, male, wild-type and Ahr-null C57BL/6J mice gavaged with either a single dose of 1000 µg/kg 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) or purely corn oil vehicle and sacrificed and harvested liver and kidneys 19 hours post-gavage. I haven not been to locate if the livers and kidneys originated with the same mice (that they are paired); so, I have treated each liver and kidney as arising from separate individual mice. The authors came to the conclusion the AhR and interactions between TCDD and the AhR regulate distinct process depending upon the organ. Additionally, they corroborated biochemical studies illustrating TCDD’s selective binding to the AhR (and I have reproduced below) TCDD, independent of AhR, elicits little to no differential mRNA expression.
For processing and modeling the microarray data, I have tried to follow the appropriate methods section of Boutros’s 2009 paper. The raw affymetrix microarray intensity values from GEO entries GSE15857 (kidney) and GSE15858 (liver) are in the data folder.
In Boutros’s paper, they used (and below I have reproduced) the following linear model in limma: \[Y = Basal + AhR + TCDD + AhR:TCDD\] where \(Y\) refers to a ProbeSet’s expression level (see next paragraph for explanation of what a ProbeSet is), \(Basal\) refers to the basal gene expression of a ProbeSet, \(AhR\) refers to the animal’s Ahr genotype, and \(TCDD\) refers to whether the animals was gavaged with 1000 µg/kg TCDD or vehicle. The final term, \(AhR:TCDD\), refers to an effect on a ProbeSet’s expression level explained by the interaction of TCDD and AhR, which makes sense since TCDD selectively binds and activates the AhR, promoting gene regulation. The linear model was fit separately for each organ’s 45,101 unique ProbeSets and for each organ, kidney and liver. After fitting the model to each Probeset, each coefficient’s p-value (for \(AhR\), \(TCDD\), and \(AhR:TCDD\)) were adjusted by the Benjamanini-Hochberg False Discovery Ratio method. This contrasts with their cited Bayesian-FDR method. Although this leads to differences in the exact number of significantly regulated ProbeSets in the liver and kidney as as response to Ahr genotype or TCDD-AhR interactions, my non-Bayesian approach produces roughly similar results.
To clarify what is a ProbeSet in an affymetrix microarray, it is composed of multiple cDNA sequences with slightly different properties that bind to the same particular gene. ProbeSets, which are specific to a gene, are represented by “[1-9]at" and those, which non-specifically cross-hybridize to non-targeted cDNAs, are represented by "[a-z]at”. Some genes have multiple ProbeSets with some specific and others potentially cross-hybridizing. Usually, they are strongly correlated but not always. Although there are ways people use to narrow down the number and variety of ProbeSets, I have not eliminated any because the effort is not worth the loss of potentially valuable information. For certain genes, non-specific ProbeSets are all that’s there: for example, Cyp1a1, the most highly upregulated ProbeSet in the kidney microarrays of wild-type mice after gavaging with 1000 µg/kg TCDD, has only one ProbeSet and it may potentially cross-hybridize (its id is 1422217_a_at).
1.1 Kidney
I performed the Boutros workflow on the kidney gene expression first.
1.1.1 Metadata pull-down
directory <- paste(parent, "data/GSE15857_RAW", sep = "/")
gset <- GEOquery::getGEO("GSE15857", GSEMatrix =TRUE)
accession <- gset$GSE15857_series_matrix.txt.gz$geo_accession
filename <- paste(accession, ".CEL", sep="")
sex <- gset$GSE15857_series_matrix.txt.gz$`gender:ch1`
tissue <- gset$GSE15857_series_matrix.txt.gz$`tissue:ch1`
Ahr <- gset$GSE15857_series_matrix.txt.gz$`ahr:ch1`
treatment <- gset$GSE15857_series_matrix.txt.gz$`treatment:ch1`
GSE15857_meta <- data.frame(cbind(filename, accession, sex, tissue, Ahr, treatment))
#kable(GSE15857_meta, table.attr = "class=\"striped\"", format = "html")
GSE15857_metarownames(GSE15857_meta) <- GSE15857_meta$filename
#fns <- list.celfiles(directory)
#fns %in% GSE15857_meta[, 1] 1.1.2 Reading in Data and Probe-dependent Normalization
Data <- ReadAffy(filenames = GSE15857_meta$filename,
phenoData = GSE15857_meta, celfile.path=directory,
compress=F,
verbose=T, cdfname = "mouse4302")
#exprs(Data)
eset <- gcrma(Data)
#exprs(eset)
eset_norm <- exprs(eset)
#dim(eset_norm)1.1.3 Cleaning and FC Calculations
## Bimap interface:
probeID <- mouse4302ACCNUM
# Get the probe identifiers that are mapped to an ACCNUM
mapped_probes <- mappedkeys(probeID)
## Bimap interface:
geneID <- mouse4302GENENAME
# Get the probe identifiers that are mapped to an ACCNUM
mapped_genes <- mappedkeys(geneID)
Symbol <- select(mouse4302.db, keys=mapped_genes, columns = c("SYMBOL"))
eset_norm_wSymbols <-
eset_norm %>%
as.data.frame() %>%
rownames_to_column(var = "PROBEID") %>%
left_join(Symbol, by = "PROBEID") %>%
dplyr::select("probeID"=PROBEID, "Symbol"=SYMBOL, everything())
## BiomaRt output -
#ensembl <- biomaRt::useEnsembl(biomart = "genes",mirror="uswest",dataset = "mmusculus_gene_ensembl")
#saveRDS(ensembl, paste(output, "ensembl.RDS", sep = "/"))
ensembl <- readRDS(paste(output, "ensembl.RDS", sep = "/"))
biomart.output <- biomaRt::getBM(mart = ensembl,
filters = "external_gene_name",
values = eset_norm_wSymbols$Symbol,
attributes =c("external_gene_name","description", "chromosome_name"),
uniqueRows = TRUE)
eset_wGeneMeta <-
eset_norm_wSymbols %>%
left_join(biomart.output, by = c("Symbol"="external_gene_name")) %>%
dplyr::select(probeID, Symbol, description, "chromosome"=chromosome_name, everything()) %>%
distinct(probeID, .keep_all = T)
GSE15857_metaNoFN <-
GSE15857_meta %>%
dplyr::select(-filename)
rownames(GSE15857_metaNoFN) <- c()
sampleInfo <- names(GSE15857_metaNoFN)
colnames(eset_wGeneMeta) <- str_remove(colnames(eset_wGeneMeta), pattern = ".CEL")
probeMeta <- c("probeID", "Symbol", "description", "chromosome")
eset_long_design <-
eset_wGeneMeta %>%
pivot_longer(-all_of(probeMeta), names_to = "accession", values_to = "expr") %>%
left_join(GSE15857_metaNoFN, by = c("accession")) %>%
dplyr::select(all_of(probeMeta), all_of(sampleInfo), everything())
FC_filtCornOil <-
eset_long_design %>%
filter(treatment=="Corn oil") %>%
group_by(Ahr, probeID) %>%
summarise(meanExpr = mean(expr)) %>%
group_by(probeID) %>%
summarise(FC = meanExpr[Ahr=="wildtype"] - meanExpr[Ahr=="knockout"]) %>%
arrange(desc(FC)) %>%
left_join(Symbol, by = c("probeID"="PROBEID")) %>%
dplyr::select(probeID, "Symbol"=SYMBOL, everything()) %>%
left_join(biomart.output, by = c("Symbol"="external_gene_name")) %>%
dplyr::select(probeID, Symbol, description, "chromosome"=chromosome_name, everything())
FC_filtTCDD <-
eset_long_design %>%
filter(treatment=="TCDD") %>%
group_by(Ahr, probeID) %>%
summarise(meanExpr = mean(expr)) %>%
group_by(probeID) %>%
summarise(FC = meanExpr[Ahr=="wildtype"] - meanExpr[Ahr=="knockout"]) %>%
arrange(desc(FC)) %>%
left_join(Symbol, by = c("probeID"="PROBEID")) %>%
dplyr::select(probeID, "Symbol"=SYMBOL, everything()) %>%
left_join(biomart.output, by = c("Symbol"="external_gene_name")) %>%
dplyr::select(probeID, Symbol, description, "chromosome"=chromosome_name, everything())
FC_filtWT <-
eset_long_design %>%
filter(Ahr == "wildtype") %>%
group_by(treatment, probeID) %>%
summarise(meanExpr = mean(expr)) %>%
group_by(probeID) %>%
summarise(FC = meanExpr[treatment=="TCDD"] - meanExpr[treatment=="Corn oil"]) %>%
arrange(desc(FC)) %>%
left_join(Symbol, by = c("probeID"="PROBEID")) %>%
dplyr::select(probeID, "Symbol"=SYMBOL, everything()) %>%
left_join(biomart.output, by = c("Symbol"="external_gene_name")) %>%
dplyr::select(probeID, Symbol, description, "chromosome"=chromosome_name, everything())
FC_filtAhrNull <-
eset_long_design %>%
filter(Ahr == "knockout") %>%
group_by(treatment, probeID) %>%
summarise(meanExpr = mean(expr)) %>%
group_by(probeID) %>%
summarise(FC = meanExpr[treatment=="TCDD"] - meanExpr[treatment=="Corn oil"]) %>%
arrange(desc(FC)) %>%
left_join(Symbol, by = c("probeID"="PROBEID")) %>%
dplyr::select(probeID, "Symbol"=SYMBOL, everything()) %>%
left_join(biomart.output, by = c("Symbol"="external_gene_name")) %>%
dplyr::select(probeID, Symbol, description, "chromosome"=chromosome_name, everything())
FC_filtWT_Ahr <-
FC_filtWT %>%
dplyr::select(probeID, FC) %>%
mutate(Ahr = "wildtype") %>%
dplyr::select(Ahr, probeID, FC)
FC_filtAhrnull_Ahr <-
FC_filtAhrNull %>%
dplyr::select(probeID, FC) %>%
mutate(Ahr = "knockout") %>%
dplyr::select(Ahr, probeID, FC)
FC_WToverKO <-
rbind(FC_filtWT_Ahr, FC_filtAhrnull_Ahr) %>%
group_by(probeID) %>%
summarise(FC = FC[Ahr == "wildtype"] - FC[Ahr == "knockout"]) %>%
arrange(desc(FC)) %>%
left_join(Symbol, by = c("probeID"="PROBEID")) %>%
dplyr::select(probeID, "Symbol"=SYMBOL, everything()) %>%
left_join(biomart.output, by = c("Symbol"="external_gene_name")) %>%
dplyr::select(probeID, Symbol, description, "chromosome"=chromosome_name, everything())
Kidney_FCs_table <-
FC_filtWT %>%
rename("FC"="FC_WT_TCDD") %>%
left_join(FC_filtAhrNull[, which(names(FC_filtAhrNull) %in% c("probeID", "FC"))], by = "probeID") %>%
rename("FC"="FC_KO_TCDD") %>%
left_join(FC_WToverKO[, which(names(FC_WToverKO) %in% c("probeID", "FC"))], by = "probeID") %>%
rename("FC"="FC_TCDD_WToverKO") %>%
left_join(FC_filtCornOil[, which(names(FC_filtCornOil) %in% c("probeID", "FC"))], by = "probeID") %>%
rename("FC"="FC_WToverKO_CornOil") %>%
left_join(FC_filtTCDD[, which(names(FC_filtTCDD) %in% c("probeID", "FC"))], by = "probeID") %>%
rename("FC"="FC_WToverKO_TCDD") %>%
distinct(probeID, .keep_all = TRUE)
#kable(Kidney_FCs_table, digits = 4, table.attr = "class=\"striped\"", format = "html")1.1.4 Principal Components 1 and 2
Kidney gene expression scores plot of first two Principal Components with squares indicating wildtype Ahr mice and circles indicating knockouts; also, red indicating mice gavaged once with 1000 µg/kg TCDD 19 hours prior to sacrifice and blue indicating a gavage with vehicle (0 µg/kg TCDD).
The kidney gene expression is primarily separated by their Ahr genotype as evident by the first Principal Component. Secondarily, it’s driven by the administration of 1000 µg/kg TCDD or vehicle.
kidney_wide_tr <-
eset_long_design %>%
dplyr::select(-Symbol, -Ahr, -treatment, -description, -chromosome, -sex, -tissue) %>%
pivot_wider(names_from = "probeID", values_from = "expr") %>%
left_join(GSE15857_metaNoFN, by="accession") %>%
dplyr::select(all_of(sampleInfo), everything())
#PCA
res.pca <- prcomp(kidney_wide_tr[,6:ncol(kidney_wide_tr)], center = TRUE)
# PCA scores
scores <-
res.pca %>%
.[["x"]] %>%
as.data.frame()
# PCs' percent explained variance
eigenAttributes <- factoextra::get_eig(res.pca)
pc1_pev <- round(eigenAttributes[1,which(names(eigenAttributes) %in% c("variance.percent"))],2)
pc2_pev <- round(eigenAttributes[2,which(names(eigenAttributes) %in% c("variance.percent"))],2)
boundaryMaxPC1 <- res.pca[["x"]] %>% as.data.frame() %>% dplyr::select(PC1) %>% max() + 1
boundaryMinPC1 <- res.pca[["x"]] %>% as.data.frame() %>% dplyr::select(PC1) %>% min() - 1
boundaryMaxPC2 <- res.pca[["x"]] %>% as.data.frame() %>% dplyr::select(PC2) %>% max() + 1
boundaryMinPC2 <- res.pca[["x"]] %>% as.data.frame() %>% dplyr::select(PC2) %>% min() - 1
width <- (boundaryMaxPC1 - boundaryMinPC1) / 2
height <- (boundaryMaxPC2 - boundaryMinPC2) / 2
#pdf(paste(directoryPlots, "Boutros_Microarray_Kidney.pdf", sep = "/"), width = width, height = height)
res.pca[["x"]] %>%
as.data.frame() %>%
cbind(kidney_wide_tr[,1:5], .) %>%
ggplot(aes(x = PC1, y = PC2, fill = treatment)) +
geom_point(aes(shape = Ahr),size=10, stroke = 2, pch=ifelse(Ahr=="knockout", 21, 22)) +
geom_hline(yintercept=0, alpha = 0.2) +
geom_vline(xintercept=0, alpha = 0.2) +
#ggrepel::geom_text_repel(aes(x = PC1, y = PC2, label = ID)) +
labs(x=bquote("PC1 ("~.(pc1_pev)~"%)"), y=bquote("PC2 ("~.(pc2_pev)~"%)")) +
scale_fill_discrete(guide = "none") +
scale_x_continuous(limits = c(boundaryMinPC1, boundaryMaxPC1)) +
scale_y_continuous(limits = c(boundaryMinPC2, boundaryMaxPC2)) +
cowplot::theme_cowplot() +
theme(legend.position = "bottom",
legend.justification = "center")
#dev.off()1.1.5 Statistical Modeling (limma)
Ahr <- as.factor(Ahr)
treatment <- as.factor(treatment)
design <- model.matrix(~ Ahr + treatment + Ahr:treatment)
fit <- lmFit(eset, design)
fit_eb <- eBayes(fit)
tt_fit_eb_ahr <-
topTable(fit_eb, number=nrow(eset_norm), coef=2, adjust="BH") %>% # Ahr
mutate(Ahr = ifelse(adj.P.Val <= 0.05, "*", "")) %>%
dplyr::select(Ahr) %>%
rownames_to_column(var="probeID")
tt_fit_eb_tcdd <-
topTable(fit_eb, number=nrow(eset_norm), coef=3, adjust="BH") %>%# TCDD
mutate(TCDD = ifelse(adj.P.Val <= 0.05, "*", "")) %>%
dplyr::select(TCDD) %>%
rownames_to_column(var="probeID")
tt_fit_eb_interaction <-
topTable(fit_eb, number=nrow(eset_norm), coef=4, adjust="BH") %>%# Interaction
mutate(Interaction = ifelse(adj.P.Val <= 0.05, "*", "")) %>%
dplyr::select(Interaction) %>%
rownames_to_column(var="probeID")
sigCombined <-
tt_fit_eb_ahr %>%
left_join(tt_fit_eb_tcdd, by = "probeID") %>%
left_join(tt_fit_eb_interaction, by = "probeID")
Kidney_FCs_table_final <-
Kidney_FCs_table %>%
left_join(sigCombined, "probeID")
folder_names <- c("parent", "directoryPlots", "output")
rm(list=ls()[! ls() %in% c("Kidney_FCs_table_final", "ensembl", folder_names)])
saveRDS(Kidney_FCs_table_final, paste(output, "Kidney_FCs_table_final.RDS", sep = "/"))
Kidney_FCs_table_final %>%
dplyr::select(probeID, Symbol, description, FC_WT_TCDD, FC_WToverKO_CornOil) %>%
arrange(desc(FC_WT_TCDD)) 1.2 Liver
Below is a reproduction of the Boutros workflow on the liver cDNA microarrays with the frequentist FDR correction instead of the Bayesian-FDR method.
1.2.1 Metadata pull-down
directory <- paste(parent, "data/GSE15858_RAW", sep = "/")
gset <- GEOquery::getGEO("GSE15858", GSEMatrix =TRUE)
accession <- gset$GSE15858_series_matrix.txt.gz$geo_accession
filename <- paste(accession, ".CEL.gz", sep="")
sex <- gset$GSE15858_series_matrix.txt.gz$`gender:ch1`
tissue <- gset$GSE15858_series_matrix.txt.gz$`tissue:ch1`
Ahr <- gset$GSE15858_series_matrix.txt.gz$`ahr:ch1`
treatment <- gset$GSE15858_series_matrix.txt.gz$`treatment:ch1`
GSE15858_meta <- data.frame(cbind(filename, accession, sex, tissue, Ahr, treatment))
GSE15858_metarownames(GSE15858_meta) <- GSE15858_meta$filename
#fns <- list.celfiles(directory)
#fns %in% GSE15858_meta[, 1] 1.2.2 Reading in Data and Probe-dependent Normalization
Data <- ReadAffy(filenames = GSE15858_meta$filename,
phenoData = GSE15858_meta, celfile.path=directory,
compress=T,
verbose=T, cdfname = "mouse4302")
#exprs(Data)
eset <- gcrma(Data)
#exprs(eset)
eset_norm <- exprs(eset)
#dim(eset_norm)1.2.3 Cleaning and FC Calculations
## Bimap interface:
probeID <- mouse4302ACCNUM
# Get the probe identifiers that are mapped to an ACCNUM
mapped_probes <- mappedkeys(probeID)
## Bimap interface:
geneID <- mouse4302GENENAME
# Get the probe identifiers that are mapped to an ACCNUM
mapped_genes <- mappedkeys(geneID)
Symbol <- select(mouse4302.db, keys=mapped_genes, columns = c("SYMBOL"))
eset_norm_wSymbols <-
eset_norm %>%
as.data.frame() %>%
rownames_to_column(var = "PROBEID") %>%
left_join(Symbol, by = "PROBEID") %>%
dplyr::select("probeID"=PROBEID, "Symbol"=SYMBOL, everything())
## BiomaRt output -
#ensembl <- biomaRt::useEnsembl(biomart = "genes",mirror="uswest",dataset = "mmusculus_gene_ensembl")
biomart.output <- biomaRt::getBM(mart = ensembl,
filters = "external_gene_name",
values = eset_norm_wSymbols$Symbol,
attributes =c("external_gene_name","description", "chromosome_name"),
uniqueRows = TRUE)
eset_wGeneMeta <-
eset_norm_wSymbols %>%
left_join(biomart.output, by = c("Symbol"="external_gene_name")) %>%
dplyr::select(probeID, Symbol, description, "chromosome"=chromosome_name, everything()) %>%
distinct()
GSE15858_metaNoFN <-
GSE15858_meta %>%
dplyr::select(-filename)
rownames(GSE15858_metaNoFN) <- c()
sampleInfo <- names(GSE15858_metaNoFN)
colnames(eset_wGeneMeta) <- str_remove(colnames(eset_wGeneMeta), pattern = ".CEL.gz")
probeMeta <- c("probeID", "Symbol", "description", "chromosome")
eset_long_design <-
eset_wGeneMeta %>%
pivot_longer(-all_of(probeMeta), names_to = "accession", values_to = "expr") %>%
left_join(GSE15858_metaNoFN, by = c("accession")) %>%
dplyr::select(all_of(probeMeta), all_of(sampleInfo), everything()) %>%
distinct()
FC_filtCornOil <-
eset_long_design %>%
filter(treatment=="Corn oil") %>%
group_by(Ahr, probeID) %>%
summarise(meanExpr = mean(expr)) %>%
group_by(probeID) %>%
summarise(FC = meanExpr[Ahr=="wildtype"] - meanExpr[Ahr=="knockout"]) %>%
arrange(desc(FC)) %>%
left_join(Symbol, by = c("probeID"="PROBEID")) %>%
dplyr::select(probeID, "Symbol"=SYMBOL, everything()) %>%
left_join(biomart.output, by = c("Symbol"="external_gene_name")) %>%
dplyr::select(probeID, Symbol, description, "chromosome"=chromosome_name, everything())
FC_filtTCDD <-
eset_long_design %>%
filter(treatment=="TCDD") %>%
group_by(Ahr, probeID) %>%
summarise(meanExpr = mean(expr)) %>%
group_by(probeID) %>%
summarise(FC = meanExpr[Ahr=="wildtype"] - meanExpr[Ahr=="knockout"]) %>%
arrange(desc(FC)) %>%
left_join(Symbol, by = c("probeID"="PROBEID")) %>%
dplyr::select(probeID, "Symbol"=SYMBOL, everything()) %>%
left_join(biomart.output, by = c("Symbol"="external_gene_name")) %>%
dplyr::select(probeID, Symbol, description, "chromosome"=chromosome_name, everything())
FC_filtWT <-
eset_long_design %>%
filter(Ahr == "wildtype") %>%
group_by(treatment, probeID) %>%
summarise(meanExpr = mean(expr)) %>%
group_by(probeID) %>%
summarise(FC = meanExpr[treatment=="TCDD"] - meanExpr[treatment=="Corn oil"]) %>%
arrange(desc(FC)) %>%
left_join(Symbol, by = c("probeID"="PROBEID")) %>%
dplyr::select(probeID, "Symbol"=SYMBOL, everything()) %>%
left_join(biomart.output, by = c("Symbol"="external_gene_name")) %>%
dplyr::select(probeID, Symbol, description, "chromosome"=chromosome_name, everything())
FC_filtAhrNull <-
eset_long_design %>%
filter(Ahr == "knockout") %>%
group_by(treatment, probeID) %>%
summarise(meanExpr = mean(expr)) %>%
group_by(probeID) %>%
summarise(FC = meanExpr[treatment=="TCDD"] - meanExpr[treatment=="Corn oil"]) %>%
arrange(desc(FC)) %>%
left_join(Symbol, by = c("probeID"="PROBEID")) %>%
dplyr::select(probeID, "Symbol"=SYMBOL, everything()) %>%
left_join(biomart.output, by = c("Symbol"="external_gene_name")) %>%
dplyr::select(probeID, Symbol, description, "chromosome"=chromosome_name, everything())
FC_filtWT_Ahr <-
FC_filtWT %>%
dplyr::select(probeID, FC) %>%
mutate(Ahr = "wildtype") %>%
dplyr::select(Ahr, probeID, FC)
FC_filtAhrnull_Ahr <-
FC_filtAhrNull %>%
dplyr::select(probeID, FC) %>%
mutate(Ahr = "knockout") %>%
dplyr::select(Ahr, probeID, FC)
FC_WToverKO <-
rbind(FC_filtWT_Ahr, FC_filtAhrnull_Ahr) %>%
group_by(probeID) %>%
summarise(FC = FC[Ahr == "wildtype"] - FC[Ahr == "knockout"]) %>%
arrange(desc(FC)) %>%
left_join(Symbol, by = c("probeID"="PROBEID")) %>%
dplyr::select(probeID, "Symbol"=SYMBOL, everything()) %>%
left_join(biomart.output, by = c("Symbol"="external_gene_name")) %>%
dplyr::select(probeID, Symbol, description, "chromosome"=chromosome_name, everything())
Liver_FCs_table <-
FC_filtWT %>%
rename("FC"="FC_WT_TCDD") %>%
left_join(FC_filtAhrNull[, which(names(FC_filtAhrNull) %in% c("probeID", "FC"))], by = "probeID") %>%
rename("FC"="FC_KO_TCDD") %>%
left_join(FC_WToverKO[, which(names(FC_WToverKO) %in% c("probeID", "FC"))], by = "probeID") %>%
rename("FC"="FC_TCDD_WToverKO") %>%
left_join(FC_filtCornOil[, which(names(FC_filtCornOil) %in% c("probeID", "FC"))], by = "probeID") %>%
rename("FC"="FC_WToverKO_CornOil") %>%
left_join(FC_filtTCDD[, which(names(FC_filtTCDD) %in% c("probeID", "FC"))], by = "probeID") %>%
rename("FC"="FC_WToverKO_TCDD") %>%
distinct(probeID, .keep_all = TRUE)1.2.4 Principal Components 1 and 2
Kidney gene expression scores plot of first two Principal Components with squares indicating wildtype Ahr mice and circles indicating knockouts; also, red indicating mice gavaged once with 1000 µg/kg TCDD 19 hours prior to sacrifice and blue indicating a gavage with vehicle (0 µg/kg TCDD).
Like the kidney, the liver gene expression is primarily separated by their Ahr genotype as evident by the first Principal Component.
Unlike the kidney, which separated wild-type mice by TCDD dose across the second Principal Component, the first Principal Component also separates the wild-type liver gene expression by TCDD dose and simultaneously fails to separate the Ahr-null mice by the same token. Whether an Ahr-null mouse has been gavaged with 1000 µg/kg TCDD or vehicle, it is more similar to an oppositely-treated Ahr-null mouse than they are to a wild-type mouse treated the same. Additionally, as one might expect, Ahr-null mice are more similar to wild-type mice gavaged with the vehicle than they are to the wild-type mice gavaged with TCDD.
liver_wide_tr <-
eset_long_design %>%
dplyr::select(probeID, accession, expr) %>%
distinct() %>%
pivot_wider(names_from = "probeID", values_from = "expr") %>%
left_join(GSE15858_metaNoFN, by="accession") %>%
dplyr::select(all_of(sampleInfo), everything())
#PCA
res.pca <- prcomp(liver_wide_tr[,6:ncol(liver_wide_tr)], center = TRUE)
# PCA scores
scores <-
res.pca %>%
.[["x"]] %>%
as.data.frame()
# PCs' percent explained variance
eigenAttributes <- factoextra::get_eig(res.pca)
pc1_pev <- round(eigenAttributes[1,which(names(eigenAttributes) %in% c("variance.percent"))],2)
pc2_pev <- round(eigenAttributes[2,which(names(eigenAttributes) %in% c("variance.percent"))],2)
boundaryMaxPC1 <- res.pca[["x"]] %>% as.data.frame() %>% dplyr::select(PC1) %>% max() + 1
boundaryMinPC1 <- res.pca[["x"]] %>% as.data.frame() %>% dplyr::select(PC1) %>% min() - 1
boundaryMaxPC2 <- res.pca[["x"]] %>% as.data.frame() %>% dplyr::select(PC2) %>% max() + 1
boundaryMinPC2 <- res.pca[["x"]] %>% as.data.frame() %>% dplyr::select(PC2) %>% min() - 1
width <- (boundaryMaxPC1 - boundaryMinPC1) / 2
height <- (boundaryMaxPC2 - boundaryMinPC2) / 2
#pdf(paste(directoryPlots, "Boutros_Microarray_Liver.pdf", sep = "/"), width = width/10, height = height/10)
res.pca %>%
.[["x"]] %>%
as.data.frame() %>%
cbind(liver_wide_tr[,1:5], .) %>%
ggplot(aes(x = PC1, y = PC2, fill = treatment, shape = Ahr)) +
geom_point(size=10, stroke = 2, pch=ifelse(Ahr=="knockout", 21, 22)) +
geom_hline(yintercept=0, alpha = 0.2) +
geom_vline(xintercept=0, alpha = 0.2) +
#ggrepel::geom_text_repel(aes(x = PC1, y = PC2, label = ID)) +
labs(x=bquote("PC1 ("~.(pc1_pev)~"%)"), y=bquote("PC2 ("~.(pc2_pev)~"%)")) +
scale_fill_discrete(guide = "none") +
scale_x_continuous(limits = c(boundaryMinPC1, boundaryMaxPC1)) +
scale_y_continuous(limits = c(boundaryMinPC2, boundaryMaxPC2)) +
cowplot::theme_cowplot() +
theme(legend.position = "bottom",
legend.justification = "center")
#dev.off()1.2.5 Statistical Modeling (limma)
Ahr <- as.factor(Ahr)
treatment <- as.factor(treatment)
design <- model.matrix(~ Ahr + treatment + Ahr:treatment)
fit <- lmFit(eset, design)
fit_eb <- eBayes(fit)
tt_fit_eb <-
topTable(fit_eb, number=nrow(eset_norm), coef=2:4) %>%
mutate(Ahr = ifelse(Ahrwildtype <= 0.05, "*", ""),
TCDD = ifelse(treatmentTCDD <= 0.05, "*", ""),
Interaction = ifelse(Ahrwildtype.treatmentTCDD <= 0.05, "*", "")) %>%
dplyr::select(Ahr, TCDD, Interaction) %>%
rownames_to_column(var="probeID")
tt_fit_eb_ahr <-
topTable(fit_eb, number=nrow(eset_norm), coef=2, adjust="BH") %>% # Ahr
mutate(Ahr = ifelse(adj.P.Val <= 0.05, "*", "")) %>%
dplyr::select(Ahr) %>%
rownames_to_column(var="probeID")
tt_fit_eb_tcdd <-
topTable(fit_eb, number=nrow(eset_norm), coef=3, adjust="BH") %>%# TCDD
mutate(TCDD = ifelse(adj.P.Val <= 0.05, "*", "")) %>%
dplyr::select(TCDD) %>%
rownames_to_column(var="probeID")
tt_fit_eb_interaction <-
topTable(fit_eb, number=nrow(eset_norm), coef=4, adjust="BH") %>%# Interaction
mutate(Interaction = ifelse(adj.P.Val <= 0.05, "*", "")) %>%
dplyr::select(Interaction) %>%
rownames_to_column(var="probeID")
sigCombined <-
tt_fit_eb_ahr %>%
left_join(tt_fit_eb_tcdd, by = "probeID") %>%
left_join(tt_fit_eb_interaction, by = "probeID")
Liver_FCs_table_final <-
Liver_FCs_table %>%
left_join(sigCombined, "probeID")
folder_names <- c("parent", "directoryPlots", "output")
rm(list=ls()[! ls() %in% c("Kidney_FCs_table_final", "Liver_FCs_table_final", "ensembl", folder_names)])
saveRDS(Liver_FCs_table_final, paste(output, "Liver_FCs_table_final.RDS", sep = "/"))
Liver_FCs_table_final %>%
dplyr::select(probeID, Symbol, description, FC_WT_TCDD, FC_WToverKO_CornOil) %>%
arrange(desc(FC_WT_TCDD)) 1.3 Comparison of Differential ProbeSets in Kidney and Liver
To compare the number of differentially regulated ProbeSets for the liver and kidney, I have focused on primarily three kinds of significantly different ProbeSets: (1) ProbeSets downregulated in Ahr knockout mice when gavaged with vehicle; (2) those upregulated in wild-type mice gavaged with either TCDD or vehicle and (3) also those downregulated. For (1), the significantly downregulated ProbeSets require a functional Ahr for endogenously-regulated gene expression, independent of TCDD. For (2) and (3), the differential ProbeSets have upregulated or downregulated gene expression as a result of TCDD activation of intact C57BL/6 Ahr alleles.
Generally, as evident by the correlation plots, the kidney and the liver’s significantly expressed genes overlap some but are not highly correlated (Ahr-responive \(r\) = 0.15; TCDD:Ahr \(r\) = 0.27).
In corroboration with the Principal Component scores, the upset plots below show the majority of the differentially expressed ProbeSets occur with respect to the status of the Ahr genotype, especially in the kidney. In each tissue, there is also an expected, large intersection of “Ahr-responsive” ProbeSets with differential ProbeSets up- or downregulated by the interaction of TCDD:AhR. The interaction of TCDD:AhR significantly affects many ProbeSets in both the kidney and liver. Very few ProbeSets are differentially expressed by TCDD alone. Between the liver and the kidney, the liver has more ProbeSets significantly regulated across conditions, which Boutros et al. attribute to the greater sequestration of TCDD in the liver than the kidney.
## Ahr regulated genes with Corn Oil FC Expression Gating
L_Ahr_Up <-
Liver_FCs_table_final %>%
filter(Ahr == "*", FC_WToverKO_CornOil < 0) %>%
distinct(probeID) %>%
drop_na() %>%
.$probeID
K_Ahr_Up <-
Kidney_FCs_table_final %>%
filter(Ahr == "*", FC_WToverKO_CornOil < 0) %>%
distinct(probeID) %>%
drop_na() %>%
.$probeID
L_Ahr_Down <-
Liver_FCs_table_final %>%
filter(Ahr == "*", FC_WToverKO_CornOil > 0) %>%
distinct(probeID) %>%
drop_na() %>%
.$probeID
K_Ahr_Down <-
Kidney_FCs_table_final %>%
filter(Ahr == "*", FC_WToverKO_CornOil > 0) %>%
distinct(probeID) %>%
drop_na() %>%
.$probeID
## TCDD-AhR regulated genes with Wildtype FC Expression Gating
L_Interx_Up <-
Liver_FCs_table_final %>%
filter(Interaction == "*", FC_WT_TCDD > 0) %>%
distinct(probeID) %>%
drop_na() %>%
.$probeID
K_Interx_Up <-
Kidney_FCs_table_final %>%
filter(Interaction == "*", FC_WT_TCDD > 0) %>%
distinct(probeID) %>%
drop_na() %>%
.$probeID
L_Interx_Down <-
Liver_FCs_table_final %>%
filter(Interaction == "*", FC_WT_TCDD < 0) %>%
distinct(probeID) %>%
drop_na() %>%
.$probeID
K_Interx_Down <-
Kidney_FCs_table_final %>%
filter(Interaction == "*", FC_WT_TCDD < 0) %>%
distinct(probeID) %>%
drop_na() %>%
.$probeID
## combining into list
TissueRegged <- list(L_Ahr_Up, K_Ahr_Up, L_Ahr_Down, K_Ahr_Down, L_Interx_Up, K_Interx_Up, L_Interx_Down, K_Interx_Down)
names(TissueRegged) <- c("Liver Ahr KO Upregulated", "Kidney Ahr KO Upregulated", "Liver Ahr KO Downregulated", "Kidney Ahr KO Downregulated", "Liver TCDD:AhR Upregulated", "Kidney TCDD:AhR Upregulated", "Liver TCDD:AhR Downregulated", "Kidney TCDD:AhR Downregulated")1.3.1 Magnitude and Percentage Differential ProbeSets in Liver and Kidney
frxn_4302 <- function(x, length.computed=FALSE){
if (length.computed) {
frxn <- x / 4101
} else {
frxn <- length(x) / 45101
}
return(frxn)
}
tissueCondDiffMag <-
lapply(TissueRegged, length) %>%
do.call(rbind, .) %>%
as.data.frame() %>%
rename("V1"="Magnitude") %>%
rownames_to_column(var="Category")
frxnDiffTissue <-
lapply(TissueRegged, frxn_4302) %>%
do.call(rbind, .) %>%
as.data.frame() %>%
rename("V1"="Fraction") %>%
rownames_to_column(var="Category") %>%
left_join(tissueCondDiffMag, by = "Category") %>%
mutate(Tissue = ifelse(str_detect(Category, "Liver"), "Liver", "Kidney"),
Category = ifelse(str_detect(Category, "Liver"),
str_remove(Category, "Liver "),
str_remove(Category, "Kidney ")),
`Fold Change` = ifelse(str_detect(Category, "Upregulated"), "Upregulated", "Downregulated"),
Category = ifelse(str_detect(Category, " Upregulated"),
str_remove(Category, " Upregulated"),
str_remove(Category, " Downregulated")),
Fraction = paste(round(Fraction, 4) * 100, "%", sep=""),
Tissue = fct_relevel(Tissue, c("Liver", "Kidney"))) %>%
dplyr::select(Tissue, Category, `Fold Change`, Magnitude, Fraction) %>%
arrange(Tissue, Category)
frxnDiffTissue 1.3.2 Fold-Change of Ahr-regulated ProbeSets across Tissues
This figure is a reproduction of FIG 4. (C) in Boutros et al, 2009. The fold-change refers to the wild-type ProbeSet signal over the Ahr-null ProbeSet signal gavaged with vehicle. The color of the points refers to if a ProbeSet was significant in the Kidney, Liver, both, or neither. To calculate the Spearman’s correlation value between Liver and Kidney gene expression, all of the ProbeSets significantly affected by the Ahr-genotype were filtered and non-significant ProbeSets were not included.
L_AhrReg <-
Liver_FCs_table_final %>%
dplyr::select(probeID, "Liver_Ahr"=Ahr, "Liver"=FC_WToverKO_CornOil)
K_AhrReg <-
Kidney_FCs_table_final %>%
dplyr::select(probeID, "Kidney_Ahr"=Ahr, "Kidney"=FC_WToverKO_CornOil)
LK_AhrReg <-
L_AhrReg %>%
left_join(K_AhrReg, by = "probeID") %>%
left_join(Liver_FCs_table_final[,which(names(Liver_FCs_table_final) %in% c("probeID", "Symbol"))], by = "probeID") %>%
mutate(Significance = case_when(
(Liver_Ahr == "*" & Kidney_Ahr == "*") ~ "Both",
(Liver_Ahr == "*" & Kidney_Ahr == "") ~ "Liver",
(Liver_Ahr == "" & Kidney_Ahr == "*") ~ "Kidney",
(Liver_Ahr == "" & Kidney_Ahr == "") ~ "Neither",
TRUE ~ "Error")) %>%
dplyr::select(probeID, Symbol, Significance, Liver, Kidney)
tissueAhrCorr <-
LK_AhrReg %>%
filter(Significance != "Neither") %>%
dplyr::select(Liver, Kidney) %>%
corrr::correlate(method = "spearman") %>%
filter(term == "Liver") %>%
mutate(Kidney = round(Kidney, 4)) %>%
.$Kidney
xMax <- K_AhrReg %>% dplyr::select(Kidney) %>% max() + 1
xMin <- K_AhrReg %>% dplyr::select(Kidney) %>% min() - 1
yMax <- L_AhrReg %>% dplyr::select(Liver) %>% max() + 1
yMin <- L_AhrReg %>% dplyr::select(Liver) %>% min() - 1
width <- (xMax - xMin) / 2
height <- (yMax - yMin) / 2
SigColors <- c("#56B4E9", "#E69F00", "#CC79A7", "#999999")
#pdf(paste(directoryPlots, "Boutros_Microarrays_LK_sigFCs_Ahr.pdf", sep = "/"), width = width+2, height = height+2)
LK_AhrReg %>%
ggplot(aes(Kidney, Liver, color=Significance, fill=Significance,
label = ifelse(Significance == "Both", Symbol, ""))) +
ggrepel::geom_text_repel(force=10) +
annotate(geom="text", x=xMax-4, y=yMin+2, label=paste("Spearman's: ", tissueAhrCorr),
size=6, fontface="bold") +
geom_hline(yintercept=0, alpha = 0.2) +
geom_vline(xintercept=0, alpha = 0.2) +
geom_point(size=5, stroke = 2, alpha = 0.5, pch=21) +
scale_color_manual(values = SigColors) +
scale_fill_manual(values = SigColors) +
geom_hline(yintercept=0, alpha = 0.2) +
geom_vline(xintercept=0, alpha = 0.2) +
cowplot::theme_cowplot() +
theme(legend.position = "bottom",
legend.justification = "center")
#dev.off()1.3.3 Fold-Change of TCDD-AhR-regulated ProbeSets across Tissues
This figure is a reproduction of FIG 4. (D) in Boutros et al, 2009. The fold-change refers to the wild-type ProbeSet signal of wild-type mice gavaged with 1000 µg/kg TCDD over wild-type mice gavaged with vehicle. The color of the points refers to if a ProbeSet was significant in the Kidney, Liver, both, or neither. To calculate the Spearman’s correlation value between Liver and Kidney gene expression, all of the ProbeSets significantly affected by the TCDD-AhR interaction were filtered and non-significant ProbeSets were not included.
L_TCDDAhrReg <-
Liver_FCs_table_final %>%
dplyr::select(probeID, "Liver_Interaction"=Interaction, "Liver"=FC_WT_TCDD)
K_TCDDAhrReg <-
Kidney_FCs_table_final %>%
dplyr::select(probeID, "Kidney_Interaction"=Interaction, "Kidney"=FC_WT_TCDD)
LK_TCDDAhrReg <-
L_TCDDAhrReg %>%
left_join(K_TCDDAhrReg, by = "probeID") %>%
mutate(Significance = case_when(
(Liver_Interaction == "*" & Kidney_Interaction == "*") ~ "Both",
(Liver_Interaction == "*" & Kidney_Interaction == "") ~ "Liver",
(Liver_Interaction == "" & Kidney_Interaction == "*") ~ "Kidney",
(Liver_Interaction == "" & Kidney_Interaction == "") ~ "Neither",
TRUE ~ "Error"
)) %>%
left_join(Liver_FCs_table_final[,which(names(Liver_FCs_table_final) %in% c("probeID", "Symbol"))], by = "probeID") %>%
dplyr::select(probeID, Symbol, Significance, Liver, Kidney)
tissueTCDDAhrCorr <-
LK_TCDDAhrReg %>%
filter(Significance != "Neither") %>%
dplyr::select(Liver, Kidney) %>%
corrr::correlate(method = "spearman") %>%
filter(term == "Liver") %>%
mutate(Kidney = round(Kidney, 4)) %>%
.$Kidney
xMax <- K_TCDDAhrReg %>% dplyr::select(Kidney) %>% max() + 1
xMin <- K_TCDDAhrReg %>% dplyr::select(Kidney) %>% min() - 1
yMax <- L_TCDDAhrReg %>% dplyr::select(Liver) %>% max() + 1
yMin <- L_TCDDAhrReg %>% dplyr::select(Liver) %>% min() - 1
width <- (xMax - xMin) / 2
height <- (yMax - yMin) / 2
SigColors <- c("#56B4E9", "#E69F00", "#CC79A7", "#999999")
#pdf(paste(directoryPlots, "Boutros_Microarrays_LK_sigFCs_TCDDAhr.pdf", sep = "/"), width = 8, height = 12)
LK_TCDDAhrReg %>%
ggplot(aes(Kidney, Liver, color=Significance, fill=Significance,
label = ifelse(Significance == "Both", Symbol, ""))) +
ggrepel::geom_text_repel(force=1) +
geom_hline(yintercept=0, alpha = 0.2) +
geom_vline(xintercept=0, alpha = 0.2) +
geom_point(size=5, stroke = 2, alpha = 0.5, pch=21) +
annotate(geom="text", x=xMax-4, y=yMin+2, label=paste("Spearman's: ", tissueTCDDAhrCorr),
size=6, fontface="bold") +
scale_color_manual(values = SigColors) +
scale_fill_manual(values = SigColors) +
geom_hline(yintercept=0, alpha = 0.2) +
geom_vline(xintercept=0, alpha = 0.2) +
cowplot::theme_cowplot() +
theme(legend.position = "bottom",
legend.justification = "center")
#dev.off()1.3.4 Similar Differential ProbeSets in Liver across Conditions
listAllLiver <- TissueRegged[c(1,3,5,7)]
upset(fromList(listAllLiver), order.by = "freq")
1.3.5 Similar Differential ProbeSets in Kidney across Conditions
listAllKidney <- TissueRegged[c(2,4,6,8)]
upset(fromList(listAllKidney), order.by = "freq")
1.3.6 Differential ProbeSets by Ahr Genotype Across Tissues
listAhrBothTissues <- TissueRegged[1:4]
upset(fromList(listAhrBothTissues), order.by = "freq")
1.3.7 Downregulated ProbeSets by Ahr Genotype Across Tissues
listAhrDownBothTissues <- TissueRegged[3:4]
upset(fromList(listAhrDownBothTissues), order.by = "freq")
1.3.8 Upregulated ProbeSets by TCDD-Ahr Interaction Across Tissues
listInterUpBothTissues <- TissueRegged[5:6]
upset(fromList(listInterUpBothTissues), order.by = "freq")
1.3.9 Downregulated ProbeSets by TCDD-Ahr Interaction Across Tissues
listInterDownBothTissues <- TissueRegged[7:8]
upset(fromList(listInterDownBothTissues), order.by = "freq")
1.4 Functional Enrichment Analysis
Using intersecting or differing significant ProbeSets across tissues, we can perform functional enrichment analysis on the corresponding gene symbols to see the pathways associated with significant expression in both the kidney and liver and each separately according to Ahr status and the administration of TCDD or vehicle.
For performing functional enrichment analysis I used the R package gProfiler2.
1.4.1 Grabbing Distinct Gene Symbols by Tissue
i_AhrUp <- intersect(L_Ahr_Up, K_Ahr_Up)
L_d_AhrUp <- setdiff(L_Ahr_Up, K_Ahr_Up)
K_d_AhrUp <- setdiff(K_Ahr_Up, L_Ahr_Up)
i_AhrDown <- intersect(L_Ahr_Down, K_Ahr_Down)
L_d_AhrDown <- setdiff(L_Ahr_Down, K_Ahr_Down)
K_d_AhrDown <- setdiff(K_Ahr_Down, L_Ahr_Down)
i_InterxUp <- intersect(L_Interx_Up, K_Interx_Up)
L_d_InterxUp <- setdiff(L_Interx_Up, K_Interx_Up)
K_d_InterxUp <- setdiff(K_Interx_Up, L_Interx_Up)
i_InterxDown <- intersect(L_Interx_Down, K_Interx_Down)
L_d_InterxDown <- setdiff(L_Interx_Down, K_Interx_Down)
K_d_InterxDown <- setdiff(K_Interx_Down, L_Interx_Down)
Symbols_AhrUp <-
i_AhrUp %>%
as.data.frame() %>%
rename("."="probeID") %>%
left_join(Liver_FCs_table_final[,which(names(Liver_FCs_table_final) %in% c("probeID", "Symbol"))], by="probeID") %>%
distinct(Symbol) %>%
drop_na()
Symbols_L_AhrUp <-
L_d_AhrUp %>%
as.data.frame() %>%
rename("."="probeID") %>%
left_join(Liver_FCs_table_final[,which(names(Liver_FCs_table_final) %in% c("probeID", "Symbol"))], by="probeID") %>%
distinct(Symbol) %>%
drop_na()
Symbols_K_AhrUp <-
K_d_AhrUp %>%
as.data.frame() %>%
rename("."="probeID") %>%
left_join(Liver_FCs_table_final[,which(names(Liver_FCs_table_final) %in% c("probeID", "Symbol"))], by="probeID") %>%
distinct(Symbol) %>%
drop_na()
Symbols_AhrDown <-
i_AhrDown %>%
as.data.frame() %>%
rename("."="probeID") %>%
left_join(Liver_FCs_table_final[,which(names(Liver_FCs_table_final) %in% c("probeID", "Symbol"))], by="probeID") %>%
distinct(Symbol) %>%
drop_na()
Symbols_L_AhrDown <-
L_d_AhrDown %>%
as.data.frame() %>%
rename("."="probeID") %>%
left_join(Liver_FCs_table_final[,which(names(Liver_FCs_table_final) %in% c("probeID", "Symbol"))], by="probeID") %>%
distinct(Symbol) %>%
drop_na()
Symbols_K_AhrDown <-
K_d_AhrDown %>%
as.data.frame() %>%
rename("."="probeID") %>%
left_join(Liver_FCs_table_final[,which(names(Liver_FCs_table_final) %in% c("probeID", "Symbol"))], by="probeID") %>%
distinct(Symbol) %>%
drop_na()
Symbols_InterxUp <-
i_InterxUp %>%
as.data.frame() %>%
rename("."="probeID") %>%
left_join(Liver_FCs_table_final[,which(names(Liver_FCs_table_final) %in% c("probeID", "Symbol"))], by="probeID") %>%
distinct(Symbol) %>%
drop_na()
Symbols_L_InterxUp <-
L_d_InterxUp %>%
as.data.frame() %>%
rename("."="probeID") %>%
left_join(Liver_FCs_table_final[,which(names(Liver_FCs_table_final) %in% c("probeID", "Symbol"))], by="probeID") %>%
distinct(Symbol) %>%
drop_na()
Symbols_K_InterxUp <-
K_d_InterxUp %>%
as.data.frame() %>%
rename("."="probeID") %>%
left_join(Liver_FCs_table_final[,which(names(Liver_FCs_table_final) %in% c("probeID", "Symbol"))], by="probeID") %>%
distinct(Symbol) %>%
drop_na()
Symbols_InterxDown <-
i_InterxDown %>%
as.data.frame() %>%
rename("."="probeID") %>%
left_join(Liver_FCs_table_final[,which(names(Liver_FCs_table_final) %in% c("probeID", "Symbol"))], by="probeID") %>%
distinct(Symbol) %>%
drop_na()
Symbols_L_InterxDown <-
L_d_InterxDown %>%
as.data.frame() %>%
rename("."="probeID") %>%
left_join(Liver_FCs_table_final[,which(names(Liver_FCs_table_final) %in% c("probeID", "Symbol"))], by="probeID") %>%
distinct(Symbol) %>%
drop_na()
Symbols_K_InterxDown <-
K_d_InterxDown %>%
as.data.frame() %>%
rename("."="probeID") %>%
left_join(Liver_FCs_table_final[,which(names(Liver_FCs_table_final) %in% c("probeID", "Symbol"))], by="probeID") %>%
distinct(Symbol) %>%
drop_na()1.4.2 gProfiler2 Functional Enrichment
## Ahr upregulated genes
AhrUp_PathwayEnrichment <-
gprofiler2::gost(query = Symbols_AhrUp$Symbol,
organism = "mmusculus",
correction_method = "fdr")
## Liver Ahr upregulated genes
AhrUp_L_PathwayEnrichment <-
gprofiler2::gost(query = Symbols_L_AhrUp$Symbol,
organism = "mmusculus",
correction_method = "fdr")
## Kidney Ahr upregulated genes
AhrUp_K_PathwayEnrichment <-
gprofiler2::gost(query = Symbols_K_AhrUp$Symbol,
organism = "mmusculus",
correction_method = "fdr")
## Ahr downregulated genes
AhrDown_PathwayEnrichment <-
gprofiler2::gost(query = Symbols_AhrDown$Symbol,
organism = "mmusculus",
correction_method = "fdr")
## Liver Ahr downregulated genes
AhrDown_L_PathwayEnrichment <-
gprofiler2::gost(query = Symbols_L_AhrDown$Symbol,
organism = "mmusculus",
correction_method = "fdr")
## Kidney Ahr downregulated genes
AhrDown_K_PathwayEnrichment <-
gprofiler2::gost(query = Symbols_K_AhrDown$Symbol,
organism = "mmusculus",
correction_method = "fdr")
## Interaction upregulated genes
InterxUp_PathwayEnrichment <-
gprofiler2::gost(query = Symbols_InterxUp$Symbol,
organism = "mmusculus",
correction_method = "fdr")
## Interaction upregulated genes
InterxUp_L_PathwayEnrichment <-
gprofiler2::gost(query = Symbols_L_InterxUp$Symbol,
organism = "mmusculus",
correction_method = "fdr")
## Interaction upregulated genes
InterxUp_K_PathwayEnrichment <-
gprofiler2::gost(query = Symbols_K_InterxUp$Symbol,
organism = "mmusculus",
correction_method = "fdr")
## Interaction downregulated genes
#InterxDown_PathwayEnrichment <-
# gprofiler2::gost(query = Symbols_InterxDown$Symbol,
# organism = "mmusculus",
# correction_method = "fdr")
## Interaction downregulated genes
InterxDown_L_PathwayEnrichment <-
gprofiler2::gost(query = Symbols_L_InterxDown$Symbol,
organism = "mmusculus",
correction_method = "fdr")
## Interaction downregulated genes
InterxDown_K_PathwayEnrichment <-
gprofiler2::gost(query = Symbols_K_InterxDown$Symbol,
organism = "mmusculus",
correction_method = "fdr")1.4.3 Functional Enrichment - Ahr Downregulated
AhrDown_PathwayEnrichment$result %>% dplyr::select(source, term_name, term_size, intersection_size)1.4.4 Functional Enrichment - Liver AhR Downregulated
AhrDown_L_PathwayEnrichment$result %>% dplyr::select(source, term_name, term_size, intersection_size)1.4.5 Functional Enrichment - Kidney AhR Downregulated
AhrDown_K_PathwayEnrichment$result %>% dplyr::select(source, term_name, term_size, intersection_size)1.4.6 Functional Enrichment - TCDD-Ahr Upregulated
InterxUp_PathwayEnrichment$result %>% dplyr::select(source, term_name, term_size, intersection_size)1.4.7 Functional Enrichment - Liver TCDD-Ahr Upregulated
InterxUp_L_PathwayEnrichment$result %>% dplyr::select(source, term_name, term_size, intersection_size)1.4.8 Functional Enrichment - Kidney TCDD-Ahr Upregulated
InterxUp_K_PathwayEnrichment$result %>% dplyr::select(source, term_name, term_size, intersection_size)1.4.9 Functional Enrichment - Liver TCDD-Ahr Downregulated
InterxDown_L_PathwayEnrichment$result %>% dplyr::select(source, term_name, term_size, intersection_size)1.4.10 Functional Enrichment - Kidney TCDD-Ahr Downregulated
InterxDown_K_PathwayEnrichment$result %>% dplyr::select(source, term_name, term_size, intersection_size)1.5 Relevance to Beaumont-HNMR Collaboration
The Boutros et al. microarrays provide a glimpse of the Ahr and TCDD-AhR mediated gene expression in the liver and kidney. In our collaboration with the Stewart lab at Beaumont Health, we have detected a dose-dependent induction of Trimethylamine N-Oxide (TMAO) and glycolate in the urine of mice gavaged every 4 days for 28 days with some dose of TCDD (0 - 30 µg/kg TCDD).
TMAO is formed when Trimethylamine (TMA), a small molecule formed by the gut microbiome, is oxidized by Flavin Monooxygenases (FMOs) and primarily by FMO3. In the Boutros et al. study design (gavaged 1000 µg/kg TCDD or vehicle 19 hours before sacrifice), Fmo3 is significantly induced 66-fold in the liver of wild-type mice treated with TCDD compared to vehicle. Fmo2, which has less TMAO-forming activity, is also significantly induced by TCDD (22-fold); additionally, it is significantly induced in Ahr null mice (1.79-fold), suggesting alternative transcription factors regulating its expression. Abcc4, a known exporter of bile acid from the liver into the bloodstream, which has been shown to export TMAO in vitro, is induced ~ 47-fold in wild-type mouse liver after 28 days of gavaging repeatedly with 30 µg/kg TCDD. However, in the Boutros wild-type livers, Abcc4 is only induced 1.47-fold. After TMAO is exported from the liver, it is cleared in the urine and be filtered by the kidney. In the same study, which showed TMAO is exported by Abcc4, TMAO was shown to be imported into kidney cells by Slc22a2, which in the Boutros kidney microarray is modestly downregulated by TCDD exposure (1.03 fold) similar to Slc47a1 (1.06-fold), which exports TMAO from renal cells. Interestingly, both transporters are downregulated in Ahr-null mice (1.21- and 1.12-fold, respectively) suggesting their expression is partly dependent on AhR-mediated kidney development.
Glycolate is formed from primarily two pathways: hydroxyproline catabolism, which occurs primarily in the liver, and glyoxal detoxification, which occurs in the liver, kidney, and other tissues. Hydroxyproline is an essential building block of collagen and has been previously been shown by Nault et al. to be dose-dependently induced in mice repeatedly gavaged with TCDD to support liver fibrosis. Maybe the most pertinent enzyme in the pathway related to glycolate, Hao1, catalyzes the formation of glyoxylate from glycolate and atmospheric oxygen with Flavin Mononucleotide (FMN). Experiments with KO models of Hao1 or a riboflavin-deficient diet in mice have shown an increase in levels of urinary glycolate levels. It is one of the most dose-dependently reduced enzymes in the liver of male mice repeatedly gavaged for 28 days with 30 µg/kg TCDD (~ 250-fold). In the wild-type livers of Boutros et al., it is more modestly reduced (1.2-fold); although it along with its peroxisomal partner Agxt and the glyoxal detoxifying enzyme Glo1 have significantly altered expression in Ahr-null liver. In the KOs, Hao1 and Glo1 are reduced 1.4 and 2.1-fold, respectively, and Agxt is induced 1.88-fold. In the wild-type kidneys of Boutros et al., Aldh2, which turns glyoxal precursors into glycolate, is induced (1.57-fold).
1.5.1 TMA-TMAO Pathway
L_TMAO_Symbols <- c("Fmo1", "Fmo2", "Fmo3", "Abcc4")
L_TMAO <-
Liver_FCs_table_final %>%
filter(Symbol %in% L_TMAO_Symbols) %>%
mutate(Tissue = "Liver") %>%
group_by(Symbol) %>%
slice_max(abs(FC_WT_TCDD), n=1) %>%
mutate(FC_WT_TCDD = 2**(FC_WT_TCDD),
FC_WToverKO_CornOil = 2**(FC_WToverKO_CornOil)) %>%
dplyr::select(Tissue, Symbol, description, "Wild-type FC" = FC_WT_TCDD, "Corn Oil FC" = FC_WToverKO_CornOil,
Ahr, TCDD, "TCDD:AhR" = Interaction) %>%
arrange(factor(Symbol, levels = L_TMAO_Symbols))
K_TMAO_Symbols <- c("Slc22a2", "Slc47a1", "Slc22a8")
K_TMAO <-
Kidney_FCs_table_final %>%
filter(Symbol %in% K_TMAO_Symbols) %>%
mutate(Tissue = "Kidney") %>%
group_by(Symbol) %>%
slice_max(abs(FC_WT_TCDD), n=1) %>%
mutate(FC_WT_TCDD = 2**(FC_WT_TCDD),
FC_WToverKO_CornOil = 2**(FC_WToverKO_CornOil)) %>%
dplyr::select(Tissue, Symbol, description, "Wild-type FC" = FC_WT_TCDD, "Corn Oil FC" = FC_WToverKO_CornOil,
Ahr, TCDD, "TCDD:AhR" = Interaction) %>%
arrange(factor(Symbol, levels = K_TMAO_Symbols))
rbind(L_TMAO, K_TMAO)1.5.2 Glycolate-producing Enzymes
L_Gly_Symbols <- c("Prodh2", "Aldh4a1", "Got2", "Hoga1", "Grhpr", "Agxt2", "Ldha", "Hao1", "Agxt", "Glo1", "Hagh", "Aldh2")
L_Gly <-
Liver_FCs_table_final %>%
filter(Symbol %in% L_Gly_Symbols) %>%
mutate(Tissue = "Liver") %>%
group_by(Symbol) %>%
slice_max(abs(FC_WT_TCDD), n=1) %>%
mutate(FC_WT_TCDD = 2**(FC_WT_TCDD),
FC_WToverKO_CornOil = 2**(FC_WToverKO_CornOil)) %>%
dplyr::select(Tissue, Symbol, description, "Wild-type FC" = FC_WT_TCDD, "Corn Oil FC" = FC_WToverKO_CornOil,
Ahr, TCDD, "TCDD:AhR" = Interaction) %>%
arrange(factor(Symbol, levels = L_Gly_Symbols))
K_Gly_Symbols <- c("Glo1", "Hagh", "Aldh2", "Slc26a6")
K_Gly <-
Kidney_FCs_table_final %>%
filter(Symbol %in% K_Gly_Symbols) %>%
mutate(Tissue = "Kidney") %>%
group_by(Symbol) %>%
slice_max(abs(FC_WT_TCDD), n=1) %>%
mutate(FC_WT_TCDD = 2**(FC_WT_TCDD),
FC_WToverKO_CornOil = 2**(FC_WToverKO_CornOil)) %>%
dplyr::select(Tissue, Symbol, description, "Wild-type FC" = FC_WT_TCDD, "Corn Oil FC" = FC_WToverKO_CornOil,
Ahr, TCDD, "TCDD:AhR" = Interaction) %>%
arrange(factor(Symbol, levels = K_Gly_Symbols))
rbind(L_Gly, K_Gly)2 Supplemental: Comparison of (FC-agnostic) Differential Probes across Tissue by Ahr Genotype and TCDD-AhR Interaction
2.1 Upset Plots of Significant Genes
sigLivAhr <- Liver_FCs_table_final[Liver_FCs_table_final$Ahr == "*", ]$probeID
sigLivTCDD <- Liver_FCs_table_final[Liver_FCs_table_final$TCDD == "*", ]$probeID
sigLivInterX <- Liver_FCs_table_final[Liver_FCs_table_final$Interaction == "*", ]$probeID
sigKidAhr <- Kidney_FCs_table_final[Kidney_FCs_table_final$Ahr == "*", ]$probeID
sigKidTCDD <- Kidney_FCs_table_final[Kidney_FCs_table_final$TCDD == "*", ]$probeID
sigKidInterX <- Kidney_FCs_table_final[Kidney_FCs_table_final$Interaction == "*", ]$probeID
listOfSigs <- list(sigLivAhr, sigLivTCDD, sigLivInterX, sigKidAhr, sigKidTCDD, sigKidInterX)
names(listOfSigs) <- c("Liver_Ahr", "Liver_TCDD", "Liver_InterX", "Kidney_Ahr", "Kidney_TCDD", "Kidney_InterX")2.1.1 TCDD-AhR Interaction with Wildtype FC Expression Gating
i_AhrUp <- intersect(L_Ahr_Up, K_Ahr_Up)
L_d_AhrUp <- setdiff(L_Ahr_Up, K_Ahr_Up)
K_d_AhrUp <- setdiff(K_Ahr_Up, L_Ahr_Up)
i_AhrDown <- intersect(L_Ahr_Down, K_Ahr_Down)
L_d_AhrDown <- setdiff(L_Ahr_Down, K_Ahr_Down)
K_d_AhrDown <- setdiff(K_Ahr_Down, L_Ahr_Down)
i_InterxUp <- intersect(L_Interx_Up, K_Interx_Up)
L_d_InterxUp <- setdiff(L_Interx_Up, K_Interx_Up)
K_d_InterxUp <- setdiff(K_Interx_Up, L_Interx_Up)
i_InterxDown <- intersect(L_Interx_Down, K_Interx_Down)
L_d_InterxDown <- setdiff(L_Interx_Down, K_Interx_Down)
K_d_InterxDown <- setdiff(K_Interx_Down, L_Interx_Down)2.1.2 Grabbing Distinct Gene Symbols by Tissue
Symbols_AhrUp <-
i_AhrUp %>%
as.data.frame() %>%
rename("."="probeID") %>%
left_join(Liver_FCs_table_final[,which(names(Liver_FCs_table_final) %in% c("probeID", "Symbol"))], by="probeID") %>%
distinct(Symbol) %>%
drop_na()
Symbols_L_AhrUp <-
L_d_AhrUp %>%
as.data.frame() %>%
rename("."="probeID") %>%
left_join(Liver_FCs_table_final[,which(names(Liver_FCs_table_final) %in% c("probeID", "Symbol"))], by="probeID") %>%
distinct(Symbol) %>%
drop_na()
Symbols_K_AhrUp <-
K_d_AhrUp %>%
as.data.frame() %>%
rename("."="probeID") %>%
left_join(Liver_FCs_table_final[,which(names(Liver_FCs_table_final) %in% c("probeID", "Symbol"))], by="probeID") %>%
distinct(Symbol) %>%
drop_na()
Symbols_AhrDown <-
i_AhrDown %>%
as.data.frame() %>%
rename("."="probeID") %>%
left_join(Liver_FCs_table_final[,which(names(Liver_FCs_table_final) %in% c("probeID", "Symbol"))], by="probeID") %>%
distinct(Symbol) %>%
drop_na()
Symbols_L_AhrDown <-
L_d_AhrDown %>%
as.data.frame() %>%
rename("."="probeID") %>%
left_join(Liver_FCs_table_final[,which(names(Liver_FCs_table_final) %in% c("probeID", "Symbol"))], by="probeID") %>%
distinct(Symbol) %>%
drop_na()
Symbols_K_AhrDown <-
K_d_AhrDown %>%
as.data.frame() %>%
rename("."="probeID") %>%
left_join(Liver_FCs_table_final[,which(names(Liver_FCs_table_final) %in% c("probeID", "Symbol"))], by="probeID") %>%
distinct(Symbol) %>%
drop_na()
Symbols_InterxUp <-
i_InterxUp %>%
as.data.frame() %>%
rename("."="probeID") %>%
left_join(Liver_FCs_table_final[,which(names(Liver_FCs_table_final) %in% c("probeID", "Symbol"))], by="probeID") %>%
distinct(Symbol) %>%
drop_na()
Symbols_L_InterxUp <-
L_d_InterxUp %>%
as.data.frame() %>%
rename("."="probeID") %>%
left_join(Liver_FCs_table_final[,which(names(Liver_FCs_table_final) %in% c("probeID", "Symbol"))], by="probeID") %>%
distinct(Symbol) %>%
drop_na()
Symbols_K_InterxUp <-
K_d_InterxUp %>%
as.data.frame() %>%
rename("."="probeID") %>%
left_join(Liver_FCs_table_final[,which(names(Liver_FCs_table_final) %in% c("probeID", "Symbol"))], by="probeID") %>%
distinct(Symbol) %>%
drop_na()
Symbols_InterxDown <-
i_InterxDown %>%
as.data.frame() %>%
rename("."="probeID") %>%
left_join(Liver_FCs_table_final[,which(names(Liver_FCs_table_final) %in% c("probeID", "Symbol"))], by="probeID") %>%
distinct(Symbol) %>%
drop_na()
Symbols_L_InterxDown <-
L_d_InterxDown %>%
as.data.frame() %>%
rename("."="probeID") %>%
left_join(Liver_FCs_table_final[,which(names(Liver_FCs_table_final) %in% c("probeID", "Symbol"))], by="probeID") %>%
distinct(Symbol) %>%
drop_na()
Symbols_K_InterxDown <-
K_d_InterxDown %>%
as.data.frame() %>%
rename("."="probeID") %>%
left_join(Liver_FCs_table_final[,which(names(Liver_FCs_table_final) %in% c("probeID", "Symbol"))], by="probeID") %>%
distinct(Symbol) %>%
drop_na()2.1.3 gProfiler2 Functional Enrichment
## Ahr upregulated genes
AhrUp_PathwayEnrichment <-
gprofiler2::gost(query = Symbols_AhrUp$Symbol,
organism = "mmusculus",
correction_method = "fdr")
## Liver Ahr upregulated genes
AhrUp_L_PathwayEnrichment <-
gprofiler2::gost(query = Symbols_L_AhrUp$Symbol,
organism = "mmusculus",
correction_method = "fdr")
## Kidney Ahr upregulated genes
AhrUp_K_PathwayEnrichment <-
gprofiler2::gost(query = Symbols_K_AhrUp$Symbol,
organism = "mmusculus",
correction_method = "fdr")
## Ahr downregulated genes
AhrDown_PathwayEnrichment <-
gprofiler2::gost(query = Symbols_AhrDown$Symbol,
organism = "mmusculus",
correction_method = "fdr")
## Liver Ahr downregulated genes
AhrDown_L_PathwayEnrichment <-
gprofiler2::gost(query = Symbols_L_AhrDown$Symbol,
organism = "mmusculus",
correction_method = "fdr")
## Kidney Ahr downregulated genes
AhrDown_K_PathwayEnrichment <-
gprofiler2::gost(query = Symbols_K_AhrDown$Symbol,
organism = "mmusculus",
correction_method = "fdr")
## Interaction upregulated genes
InterxUp_PathwayEnrichment <-
gprofiler2::gost(query = Symbols_InterxUp$Symbol,
organism = "mmusculus",
correction_method = "fdr")
## Interaction upregulated genes
InterxUp_L_PathwayEnrichment <-
gprofiler2::gost(query = Symbols_L_InterxUp$Symbol,
organism = "mmusculus",
correction_method = "fdr")
## Interaction upregulated genes
InterxUp_K_PathwayEnrichment <-
gprofiler2::gost(query = Symbols_K_InterxUp$Symbol,
organism = "mmusculus",
correction_method = "fdr")
## Interaction downregulated genes
#InterxDown_PathwayEnrichment <-
# gprofiler2::gost(query = Symbols_InterxDown$Symbol,
# organism = "mmusculus",
# correction_method = "fdr")
## Interaction downregulated genes
InterxDown_L_PathwayEnrichment <-
gprofiler2::gost(query = Symbols_L_InterxDown$Symbol,
organism = "mmusculus",
correction_method = "fdr")
## Interaction downregulated genes
InterxDown_K_PathwayEnrichment <-
gprofiler2::gost(query = Symbols_K_InterxDown$Symbol,
organism = "mmusculus",
correction_method = "fdr")2.1.4 In the Liver
listOfSigsLiv <- listOfSigs[1:3]
upset(fromList(listOfSigsLiv), order.by = "freq")
2.1.5 In the Kidney
listOfSigsKid <- listOfSigs[4:6]
upset(fromList(listOfSigsKid), order.by = "freq")
2.1.6 By Ahr Genotype
Altered_Ahr <- listOfSigs[c(1, 4)]
upset(fromList(Altered_Ahr), order.by = "freq")
2.1.7 By Interaction of Genotype and TCDD
Altered_Interaction <- listOfSigs[c(3, 6)]
upset(fromList(Altered_Interaction), order.by = "freq")
2.2 Upset plots of Significant Pathways
2.2.1 Grabbing Distinct Gene Symbols by Tissue
Symbols_sigLivAhr <-
sigLivAhr %>%
as.data.frame() %>%
rename("."="probeID") %>%
left_join(Liver_FCs_table_final[,which(names(Liver_FCs_table_final) %in% c("probeID", "Symbol"))], by="probeID") %>%
distinct(Symbol) %>%
drop_na()
Symbols_sigLivInterX <-
sigLivInterX %>%
as.data.frame() %>%
rename("."="probeID") %>%
left_join(Liver_FCs_table_final[,which(names(Liver_FCs_table_final) %in% c("probeID", "Symbol"))], by="probeID") %>%
distinct(Symbol) %>%
drop_na()
Symbols_sigKidAhr <-
sigKidAhr %>%
as.data.frame() %>%
rename("."="probeID") %>%
left_join(Liver_FCs_table_final[,which(names(Liver_FCs_table_final) %in% c("probeID", "Symbol"))], by="probeID") %>%
distinct(Symbol) %>%
drop_na()
Symbols_sigKidInterX <-
sigKidInterX %>%
as.data.frame() %>%
rename("."="probeID") %>%
left_join(Liver_FCs_table_final[,which(names(Liver_FCs_table_final) %in% c("probeID", "Symbol"))], by="probeID") %>%
distinct(Symbol) %>%
drop_na()2.2.2 Grabbing Distinct Gene Symbols by Genotype
names(Altered_Ahr) <- c("L", "K")
i_sigAhr <- intersect(Altered_Ahr[["L"]], Altered_Ahr[["K"]])
L_d_sigAhr <- setdiff(Altered_Ahr[["L"]], Altered_Ahr[["K"]])
K_d_sigAhr <- setdiff(Altered_Ahr[["K"]], Altered_Ahr[["L"]])
Symbols_i_sigAhr <-
i_sigAhr %>%
as.data.frame() %>%
rename("."="probeID") %>%
left_join(Liver_FCs_table_final[,which(names(Liver_FCs_table_final) %in% c("probeID", "Symbol"))], by="probeID") %>%
distinct(Symbol) %>%
drop_na()
Symbols_L_d_sigAhr <-
L_d_sigAhr %>%
as.data.frame() %>%
rename("."="probeID") %>%
left_join(Liver_FCs_table_final[,which(names(Liver_FCs_table_final) %in% c("probeID", "Symbol"))], by="probeID") %>%
distinct(Symbol) %>%
drop_na()
Symbols_K_d_sigAhr <-
K_d_sigAhr %>%
as.data.frame() %>%
rename("."="probeID") %>%
left_join(Liver_FCs_table_final[,which(names(Liver_FCs_table_final) %in% c("probeID", "Symbol"))], by="probeID") %>%
distinct(Symbol) %>%
drop_na()2.2.3 Grabbing Distinct Gene Symbols by Interaction
names(Altered_Interaction) <- c("L", "K")
i_sigInterx <- intersect(Altered_Interaction[["L"]], Altered_Interaction[["K"]])
L_d_sigInterx <- setdiff(Altered_Interaction[["L"]], Altered_Interaction[["K"]])
K_d_sigInterx <- setdiff(Altered_Interaction[["K"]], Altered_Interaction[["L"]])
Symbols_i_sigInterx <-
i_sigInterx %>%
as.data.frame() %>%
rename("."="probeID") %>%
left_join(Liver_FCs_table_final[,which(names(Liver_FCs_table_final) %in% c("probeID", "Symbol"))], by="probeID") %>%
distinct(Symbol) %>%
drop_na()
Symbols_L_d_sigInterx <-
L_d_sigInterx %>%
as.data.frame() %>%
rename("."="probeID") %>%
left_join(Liver_FCs_table_final[,which(names(Liver_FCs_table_final) %in% c("probeID", "Symbol"))], by="probeID") %>%
distinct(Symbol) %>%
drop_na()
Symbols_K_d_sigInterx <-
K_d_sigInterx %>%
as.data.frame() %>%
rename("."="probeID") %>%
left_join(Liver_FCs_table_final[,which(names(Liver_FCs_table_final) %in% c("probeID", "Symbol"))], by="probeID") %>%
distinct(Symbol) %>%
drop_na()2.2.4 gProfiler2 Functional Enrichment
## Liver Ahr genetype and interaction
Liver_Ahr_PathwayEnrichment <-
gprofiler2::gost(query = Symbols_sigLivAhr$Symbol,
organism = "mmusculus",
correction_method = "fdr")
Liver_Interx_PathwayEnrichment <-
gprofiler2::gost(query = Symbols_sigLivInterX$Symbol,
organism = "mmusculus",
correction_method = "fdr")
## Kidney Ahr genetype and interaction
Kidney_Ahr_PathwayEnrichment <-
gprofiler2::gost(query = Symbols_sigKidAhr$Symbol,
organism = "mmusculus",
correction_method = "fdr")
Kidney_Interx_PathwayEnrichment <-
gprofiler2::gost(query = Symbols_sigKidInterX$Symbol,
organism = "mmusculus",
correction_method = "fdr")
## Same Ahr regulated genes across tissue
TissueIntersect_Ahr_PathwayEnrichment <-
gprofiler2::gost(query = Symbols_i_sigAhr$Symbol,
organism = "mmusculus",
correction_method = "fdr")
## Diff Ahr regulated genes in liver
Diff_Liver_Ahr_PathwayEnrichment <-
gprofiler2::gost(query = Symbols_L_d_sigAhr$Symbol,
organism = "mmusculus",
correction_method = "fdr")
## Diff Ahr regulated genes in kidney
Diff_Kidney_Ahr_PathwayEnrichment <-
gprofiler2::gost(query = Symbols_K_d_sigAhr$Symbol,
organism = "mmusculus",
correction_method = "fdr")
## Same TCDD-Ahr regulated genes across tissue
TissueIntersect_Interx_PathwayEnrichment <-
gprofiler2::gost(query = Symbols_i_sigInterx$Symbol,
organism = "mmusculus",
correction_method = "fdr")
## Diff TCDD-Ahr regulated genes in liver
Diff_Liver_Interx_PathwayEnrichment <-
gprofiler2::gost(query = Symbols_L_d_sigInterx$Symbol,
organism = "mmusculus",
correction_method = "fdr")
## Diff TCDD-Ahr regulated genes in kidney
Diff_Kidney_Interx_PathwayEnrichment <-
gprofiler2::gost(query = Symbols_K_d_sigInterx$Symbol,
organism = "mmusculus",
correction_method = "fdr")2.2.5 Functional Enrichment - Liver Ahr Regulated
kable(Liver_Ahr_PathwayEnrichment$result %>% dplyr::select(source, term_name, term_size, intersection_size),
table.attr = "class=\"striped\"", format = "html")| source | term_name | term_size | intersection_size |
|---|---|---|---|
| GO:BP | small molecule metabolic process | 1713 | 131 |
| GO:BP | organic acid metabolic process | 944 | 90 |
| GO:BP | carboxylic acid metabolic process | 896 | 86 |
| GO:BP | oxoacid metabolic process | 908 | 86 |
| GO:BP | monocarboxylic acid metabolic process | 616 | 56 |
| GO:BP | lipid metabolic process | 1344 | 83 |
| GO:BP | small molecule biosynthetic process | 617 | 50 |
| GO:BP | cellular amino acid metabolic process | 253 | 32 |
| GO:BP | organic acid biosynthetic process | 290 | 34 |
| GO:BP | metabolic process | 11429 | 324 |
| GO:BP | alpha-amino acid metabolic process | 182 | 27 |
| GO:BP | cellular lipid metabolic process | 994 | 64 |
| GO:BP | cellular catabolic process | 2059 | 99 |
| GO:BP | obsolete oxidation-reduction process | 548 | 45 |
| GO:BP | carboxylic acid biosynthetic process | 282 | 32 |
| GO:BP | catabolic process | 2399 | 108 |
| GO:BP | carboxylic acid catabolic process | 221 | 28 |
| GO:BP | organic acid catabolic process | 228 | 28 |
| GO:BP | fatty acid metabolic process | 425 | 38 |
| GO:BP | small molecule catabolic process | 346 | 34 |
| GO:BP | cellular metabolic process | 10350 | 296 |
| GO:BP | hormone metabolic process | 219 | 26 |
| GO:BP | organonitrogen compound metabolic process | 6326 | 204 |
| GO:BP | organic substance catabolic process | 1985 | 89 |
| GO:BP | cellular amino acid catabolic process | 92 | 17 |
| GO:BP | organic substance metabolic process | 10989 | 303 |
| GO:BP | alpha-amino acid catabolic process | 80 | 15 |
| GO:BP | cellular modified amino acid metabolic process | 179 | 21 |
| GO:BP | regulation of hormone levels | 559 | 38 |
| GO:BP | alpha-amino acid biosynthetic process | 62 | 13 |
| GO:BP | organic hydroxy compound metabolic process | 527 | 36 |
| GO:BP | response to hormone | 912 | 50 |
| GO:BP | sulfur compound metabolic process | 317 | 27 |
| GO:BP | carbohydrate derivative metabolic process | 975 | 51 |
| GO:BP | response to endogenous stimulus | 1619 | 71 |
| GO:BP | cellular hormone metabolic process | 135 | 17 |
| GO:BP | regulation of biological quality | 3876 | 132 |
| GO:BP | organophosphate metabolic process | 891 | 47 |
| GO:BP | primary metabolic process | 10243 | 276 |
| GO:BP | lipid biosynthetic process | 647 | 38 |
| GO:BP | generation of precursor metabolites and energy | 446 | 30 |
| GO:BP | response to oxygen-containing compound | 1820 | 74 |
| GO:BP | steroid metabolic process | 306 | 24 |
| GO:BP | cellular amino acid biosynthetic process | 62 | 11 |
| GO:BP | alcohol metabolic process | 344 | 25 |
| GO:BP | carbohydrate metabolic process | 587 | 34 |
| GO:BP | aromatic amino acid family metabolic process | 30 | 8 |
| GO:BP | monocarboxylic acid biosynthetic process | 194 | 18 |
| GO:BP | tyrosine metabolic process | 14 | 6 |
| GO:BP | organic substance transport | 2416 | 88 |
| GO:BP | localization | 6168 | 180 |
| GO:BP | acylglycerol metabolic process | 143 | 15 |
| GO:BP | cellular response to chemical stimulus | 3097 | 105 |
| GO:BP | transport | 4502 | 140 |
| GO:BP | neutral lipid metabolic process | 145 | 15 |
| GO:BP | nucleobase-containing small molecule metabolic process | 537 | 31 |
| GO:BP | establishment of localization | 4658 | 143 |
| GO:BP | organonitrogen compound biosynthetic process | 1570 | 63 |
| GO:BP | cellular ketone metabolic process | 213 | 18 |
| GO:BP | triglyceride metabolic process | 112 | 13 |
| GO:BP | liver development | 173 | 16 |
| GO:BP | regulation of lipid metabolic process | 361 | 24 |
| GO:BP | monosaccharide biosynthetic process | 96 | 12 |
| GO:BP | unsaturated fatty acid metabolic process | 133 | 14 |
| GO:BP | monosaccharide metabolic process | 266 | 20 |
| GO:BP | hepaticobiliary system development | 176 | 16 |
| GO:BP | organonitrogen compound catabolic process | 1249 | 53 |
| GO:BP | nucleoside phosphate metabolic process | 476 | 28 |
| GO:BP | protein catabolic process in the vacuole | 18 | 6 |
| GO:BP | response to organonitrogen compound | 1093 | 48 |
| GO:BP | drug metabolic process | 68 | 10 |
| GO:BP | glutathione metabolic process | 70 | 10 |
| GO:BP | response to wounding | 517 | 29 |
| GO:BP | response to organic cyclic compound | 1043 | 46 |
| GO:BP | cellular amide metabolic process | 1077 | 47 |
| GO:BP | regulation of hydrolase activity | 1183 | 50 |
| GO:BP | aspartate family amino acid metabolic process | 43 | 8 |
| GO:BP | lipid catabolic process | 335 | 22 |
| GO:BP | organophosphate biosynthetic process | 500 | 28 |
| GO:BP | phosphate-containing compound metabolic process | 2809 | 94 |
| GO:BP | dicarboxylic acid metabolic process | 92 | 11 |
| GO:BP | response to nitrogen compound | 1199 | 50 |
| GO:BP | liver morphogenesis | 32 | 7 |
| GO:BP | response to organic substance | 3418 | 109 |
| GO:BP | regulation of peptidase activity | 480 | 27 |
| GO:BP | positive regulation of lipid metabolic process | 174 | 15 |
| GO:BP | cellular process | 17828 | 410 |
| GO:BP | phosphorus metabolic process | 2832 | 94 |
| GO:BP | response to external stimulus | 2912 | 96 |
| GO:BP | hexose metabolic process | 247 | 18 |
| GO:BP | long-chain fatty acid metabolic process | 115 | 12 |
| GO:BP | response to drug | 459 | 26 |
| GO:BP | response to stress | 3817 | 118 |
| GO:BP | regulation of small molecule metabolic process | 355 | 22 |
| GO:BP | nucleotide metabolic process | 466 | 26 |
| GO:BP | ribose phosphate metabolic process | 385 | 23 |
| GO:BP | homeostatic process | 1922 | 69 |
| GO:BP | aspartate family amino acid catabolic process | 15 | 5 |
| GO:BP | cellular carbohydrate metabolic process | 310 | 20 |
| GO:BP | detoxification | 123 | 12 |
| GO:BP | transmembrane transport | 1533 | 58 |
| GO:BP | regulation of endopeptidase activity | 451 | 25 |
| GO:BP | cellular response to hormone stimulus | 600 | 30 |
| GO:BP | lysosomal protein catabolic process | 16 | 5 |
| GO:BP | aromatic amino acid family catabolic process | 16 | 5 |
| GO:BP | cell death | 2136 | 74 |
| GO:BP | response to toxic substance | 240 | 17 |
| GO:BP | gland development | 513 | 27 |
| GO:BP | cellular response to xenobiotic stimulus | 106 | 11 |
| GO:BP | regulation of inflammatory response | 347 | 21 |
| GO:BP | primary alcohol metabolic process | 90 | 10 |
| GO:BP | response to steroid hormone | 352 | 21 |
| GO:BP | wound healing | 380 | 22 |
| GO:BP | regulation of cell population proliferation | 1753 | 63 |
| GO:BP | regulation of glucose metabolic process | 133 | 12 |
| GO:BP | cellular response to endogenous stimulus | 1333 | 51 |
| GO:BP | hepatocyte proliferation | 30 | 6 |
| GO:BP | epithelial cell proliferation involved in liver morphogenesis | 30 | 6 |
| GO:BP | response to xenobiotic stimulus | 115 | 11 |
| GO:BP | L-ascorbic acid biosynthetic process | 4 | 3 |
| GO:BP | macromolecule localization | 2897 | 92 |
| GO:BP | nucleoside phosphate biosynthetic process | 232 | 16 |
| GO:BP | mammary gland epithelial cell proliferation | 31 | 6 |
| GO:BP | glutamate metabolic process | 31 | 6 |
| GO:BP | carbohydrate biosynthetic process | 209 | 15 |
| GO:BP | secondary alcohol metabolic process | 141 | 12 |
| GO:BP | organic cyclic compound catabolic process | 458 | 24 |
| GO:BP | glucose metabolic process | 212 | 15 |
| GO:BP | nicotinamide nucleotide biosynthetic process | 20 | 5 |
| GO:BP | pyridine nucleotide biosynthetic process | 20 | 5 |
| GO:BP | organic anion transport | 372 | 21 |
| GO:BP | nitrogen compound transport | 1986 | 68 |
| GO:BP | cellular lipid catabolic process | 214 | 15 |
| GO:BP | monocarboxylic acid catabolic process | 122 | 11 |
| GO:BP | nitric oxide metabolic process | 82 | 9 |
| GO:BP | response to nutrient levels | 523 | 26 |
| GO:BP | regulation of cellular carbohydrate metabolic process | 167 | 13 |
| GO:BP | ribonucleotide metabolic process | 376 | 21 |
| GO:BP | gland morphogenesis | 144 | 12 |
| GO:BP | xenobiotic metabolic process | 102 | 10 |
| GO:BP | response to lipid | 980 | 40 |
| GO:BP | cellular response to nutrient levels | 217 | 15 |
| GO:BP | negative regulation of proteolysis | 379 | 21 |
| GO:BP | olefinic compound metabolic process | 124 | 11 |
| GO:BP | response to extracellular stimulus | 559 | 27 |
| GO:BP | regulation of cell death | 1740 | 61 |
| GO:BP | reactive nitrogen species metabolic process | 84 | 9 |
| GO:BP | response to peptide | 531 | 26 |
| GO:BP | glycerolipid metabolic process | 384 | 21 |
| GO:BP | pigment metabolic process | 68 | 8 |
| GO:BP | ion transport | 1572 | 56 |
| GO:BP | cholesterol metabolic process | 129 | 11 |
| GO:BP | negative regulation of endopeptidase activity | 278 | 17 |
| GO:BP | cellular response to extracellular stimulus | 252 | 16 |
| GO:BP | lipid storage | 88 | 9 |
| GO:BP | pyridine-containing compound biosynthetic process | 23 | 5 |
| GO:BP | regulation of protein exit from endoplasmic reticulum | 23 | 5 |
| GO:BP | regulation of response to stress | 1254 | 47 |
| GO:BP | negative regulation of biological process | 5544 | 153 |
| GO:BP | response to peptide hormone | 452 | 23 |
| GO:BP | arachidonic acid metabolic process | 70 | 8 |
| GO:BP | nitrogen compound metabolic process | 9669 | 244 |
| GO:BP | regulation of multicellular organismal process | 2788 | 87 |
| GO:BP | hexose biosynthetic process | 90 | 9 |
| GO:BP | regulation of developmental process | 2591 | 82 |
| GO:BP | retinoid metabolic process | 71 | 8 |
| GO:BP | animal organ regeneration | 91 | 9 |
| GO:BP | regulation of proteolysis | 778 | 33 |
| GO:BP | icosanoid metabolic process | 134 | 11 |
| GO:BP | positive regulation of inflammatory response | 134 | 11 |
| GO:BP | positive regulation of lipid biosynthetic process | 91 | 9 |
| GO:BP | regeneration | 232 | 15 |
| GO:BP | lipid localization | 459 | 23 |
| GO:BP | programmed cell death | 1975 | 66 |
| GO:BP | negative regulation of peptidase activity | 287 | 17 |
| GO:BP | biosynthetic process | 5882 | 160 |
| GO:BP | aromatic compound catabolic process | 432 | 22 |
| GO:BP | glomerular filtration | 25 | 5 |
| GO:BP | fatty acid oxidation | 114 | 10 |
| GO:BP | triglyceride biosynthetic process | 39 | 6 |
| GO:BP | negative regulation of cellular process | 5068 | 141 |
| GO:BP | sterol metabolic process | 137 | 11 |
| GO:BP | complement activation, alternative pathway | 14 | 4 |
| GO:BP | positive regulation of response to wounding | 74 | 8 |
| GO:BP | pyruvate biosynthetic process | 6 | 3 |
| GO:BP | chemical homeostasis | 1245 | 46 |
| GO:BP | cell population proliferation | 2072 | 68 |
| GO:BP | response to nutrient | 187 | 13 |
| GO:BP | renal filtration | 26 | 5 |
| GO:BP | cellular response to external stimulus | 322 | 18 |
| GO:BP | regulation of response to wounding | 165 | 12 |
| GO:BP | regulation of programmed cell death | 1587 | 55 |
| GO:BP | diterpenoid metabolic process | 77 | 8 |
| GO:BP | nitric oxide biosynthetic process | 77 | 8 |
| GO:BP | regulation of response to external stimulus | 904 | 36 |
| GO:BP | lipid homeostasis | 167 | 12 |
| GO:BP | lipid oxidation | 120 | 10 |
| GO:BP | protein exit from endoplasmic reticulum | 42 | 6 |
| GO:BP | purine ribonucleotide metabolic process | 358 | 19 |
| GO:BP | negative regulation of cell death | 1119 | 42 |
| GO:BP | response to metal ion | 388 | 20 |
| GO:BP | fatty acid catabolic process | 99 | 9 |
| GO:BP | cellular response to organonitrogen compound | 643 | 28 |
| GO:BP | cellular response to nitrogen compound | 710 | 30 |
| GO:BP | secondary metabolic process | 61 | 7 |
| GO:BP | negative regulation of protein metabolic process | 1128 | 42 |
| GO:BP | positive regulation of steroid hormone biosynthetic process | 7 | 3 |
| GO:BP | L-ascorbic acid metabolic process | 7 | 3 |
| GO:BP | regulation of body fluid levels | 364 | 19 |
| GO:BP | nicotinamide nucleotide metabolic process | 29 | 5 |
| GO:BP | pyridine nucleotide metabolic process | 29 | 5 |
| GO:BP | negative regulation of hydrolase activity | 457 | 22 |
| GO:BP | regulation of carbohydrate metabolic process | 199 | 13 |
| GO:BP | cellular response to oxygen-containing compound | 1247 | 45 |
| GO:BP | regulation of wound healing | 126 | 10 |
| GO:BP | hormone biosynthetic process | 63 | 7 |
| GO:BP | positive regulation of hydrolase activity | 653 | 28 |
| GO:BP | negative regulation of cellular protein metabolic process | 1068 | 40 |
| GO:BP | glutamine family amino acid biosynthetic process | 17 | 4 |
| GO:BP | fatty acid biosynthetic process | 151 | 11 |
| GO:BP | response to glucocorticoid | 176 | 12 |
| GO:BP | nucleotide biosynthetic process | 229 | 14 |
| GO:BP | anion transport | 529 | 24 |
| GO:BP | terpenoid metabolic process | 85 | 8 |
| GO:BP | sarcosine metabolic process | 2 | 2 |
| GO:BP | regulation of transcription from RNA polymerase II promoter in response to iron | 2 | 2 |
| GO:BP | retinol metabolic process | 47 | 6 |
| GO:BP | response to gonadotropin | 31 | 5 |
| GO:BP | purine-containing compound metabolic process | 406 | 20 |
| GO:BP | xenobiotic detoxification by transmembrane export across the plasma membrane | 8 | 3 |
| GO:BP | erythrose 4-phosphate/phosphoenolpyruvate family amino acid catabolic process | 8 | 3 |
| GO:BP | regulation of phagocytosis | 108 | 9 |
| GO:BP | glycosyl compound metabolic process | 86 | 8 |
| GO:BP | ketone catabolic process | 18 | 4 |
| GO:BP | malate metabolic process | 8 | 3 |
| GO:BP | L-phenylalanine catabolic process | 8 | 3 |
| GO:BP | inflammatory response | 732 | 30 |
| GO:BP | neutral lipid biosynthetic process | 48 | 6 |
| GO:BP | acylglycerol biosynthetic process | 48 | 6 |
| GO:BP | carbohydrate derivative catabolic process | 156 | 11 |
| GO:BP | response to chemical | 5544 | 149 |
| GO:BP | gluconeogenesis | 87 | 8 |
| GO:BP | response to inorganic substance | 604 | 26 |
| GO:BP | positive regulation of response to stimulus | 2198 | 69 |
| GO:BP | pyridine-containing compound metabolic process | 33 | 5 |
| GO:BP | endoplasmic reticulum tubular network organization | 19 | 4 |
| GO:BP | enzyme linked receptor protein signaling pathway | 916 | 35 |
| GO:BP | regulation of mammary gland epithelial cell proliferation | 19 | 4 |
| GO:BP | sulfur amino acid metabolic process | 33 | 5 |
| GO:BP | response to copper ion | 33 | 5 |
| GO:BP | regulation of defense response | 575 | 25 |
| GO:BP | purine nucleotide metabolic process | 385 | 19 |
| GO:BP | steroid biosynthetic process | 161 | 11 |
| GO:BP | regulation of cysteine-type endopeptidase activity involved in apoptotic process | 214 | 13 |
| GO:BP | regulation of apoptotic process | 1550 | 52 |
| GO:BP | vitamin metabolic process | 70 | 7 |
| GO:BP | bile acid and bile salt transport | 34 | 5 |
| GO:BP | negative regulation of cell population proliferation | 715 | 29 |
| GO:BP | epithelial fluid transport | 9 | 3 |
| GO:BP | regulation of epithelial cell proliferation | 359 | 18 |
| GO:BP | erythrose 4-phosphate/phosphoenolpyruvate family amino acid metabolic process | 9 | 3 |
| GO:BP | development of secondary female sexual characteristics | 9 | 3 |
| GO:BP | L-phenylalanine metabolic process | 9 | 3 |
| GO:BP | pyruvate metabolic process | 114 | 9 |
| GO:BP | cellular response to copper ion | 20 | 4 |
| GO:BP | response to stilbenoid | 20 | 4 |
| GO:BP | glutamine family amino acid metabolic process | 71 | 7 |
| GO:BP | regulation of triglyceride metabolic process | 52 | 6 |
| GO:BP | epithelial cell proliferation | 424 | 20 |
| GO:BP | protein-containing complex subunit organization | 1636 | 54 |
| GO:BP | intracellular transport | 1409 | 48 |
| GO:BP | transmembrane receptor protein tyrosine kinase signaling pathway | 587 | 25 |
| GO:BP | regulation of ERBB signaling pathway | 73 | 7 |
| GO:BP | quinone metabolic process | 36 | 5 |
| GO:BP | positive regulation of ERBB signaling pathway | 36 | 5 |
| GO:BP | apoptotic process | 1919 | 61 |
| GO:BP | response to corticosteroid | 194 | 12 |
| GO:BP | protein homotetramerization | 54 | 6 |
| GO:BP | water-soluble vitamin biosynthetic process | 10 | 3 |
| GO:BP | protein-containing complex assembly | 1462 | 49 |
| GO:BP | negative regulation of cell maturation | 10 | 3 |
| GO:BP | cellular response to peptide | 370 | 18 |
| GO:BP | positive regulation of sister chromatid cohesion | 10 | 3 |
| GO:BP | porphyrin-containing compound metabolic process | 37 | 5 |
| GO:BP | mammary gland development | 170 | 11 |
| GO:BP | serine family amino acid metabolic process | 37 | 5 |
| GO:BP | regulation of lipid storage | 55 | 6 |
| GO:BP | positive regulation of wound healing | 55 | 6 |
| GO:BP | vitamin biosynthetic process | 22 | 4 |
| GO:BP | regulation of fatty acid beta-oxidation | 22 | 4 |
| GO:BP | regulation of hepatocyte proliferation | 22 | 4 |
| GO:BP | positive regulation of biological process | 6305 | 164 |
| GO:BP | positive regulation of phagocytosis | 76 | 7 |
| GO:BP | NADP metabolic process | 38 | 5 |
| GO:BP | organic substance biosynthetic process | 5779 | 152 |
| GO:BP | positive regulation of defense response | 256 | 14 |
| GO:BP | temperature homeostasis | 173 | 11 |
| GO:BP | regulation of fatty acid metabolic process | 99 | 8 |
| GO:BP | positive regulation of lipid storage | 23 | 4 |
| GO:BP | aspartate family amino acid biosynthetic process | 23 | 4 |
| GO:BP | macrophage migration | 57 | 6 |
| GO:BP | chylomicron remodeling | 3 | 2 |
| GO:BP | fumarate metabolic process | 3 | 2 |
| GO:BP | ribose phosphate biosynthetic process | 175 | 11 |
| GO:BP | isoleucine biosynthetic process | 3 | 2 |
| GO:BP | low-density lipoprotein particle mediated signaling | 3 | 2 |
| GO:BP | ammonia assimilation cycle | 3 | 2 |
| GO:BP | lipoprotein particle mediated signaling | 3 | 2 |
| GO:BP | cellular nitrogen compound catabolic process | 411 | 19 |
| GO:BP | regulation of immune system process | 1406 | 47 |
| GO:BP | system development | 4876 | 131 |
| GO:BP | kynurenine metabolic process | 11 | 3 |
| GO:BP | regulation of response to stimulus | 3851 | 107 |
| GO:BP | xenobiotic transport | 40 | 5 |
| GO:BP | regulation of renal system process | 40 | 5 |
| GO:BP | response to oxidative stress | 447 | 20 |
| GO:BP | regulation of platelet-derived growth factor receptor signaling pathway | 24 | 4 |
| GO:BP | glutamine metabolic process | 24 | 4 |
| GO:BP | negative regulation of programmed cell death | 1002 | 36 |
| GO:BP | regulation of protein-containing complex assembly | 448 | 20 |
| GO:BP | positive regulation of transport | 1005 | 36 |
| GO:BP | regulation of cell differentiation | 1649 | 53 |
| GO:BP | protein transport | 1535 | 50 |
| GO:BP | cellular response to drug | 81 | 7 |
| GO:BP | regulation of cysteine-type endopeptidase activity | 237 | 13 |
| GO:BP | CDP-diacylglycerol biosynthetic process | 12 | 3 |
| GO:BP | development of secondary sexual characteristics | 12 | 3 |
| GO:BP | organic acid transport | 327 | 16 |
| GO:BP | carboxylic acid transport | 297 | 15 |
| GO:BP | response to estradiol | 155 | 10 |
| GO:BP | regulation of glomerular filtration | 12 | 3 |
| GO:BP | protein tetramerization | 82 | 7 |
| GO:BP | positive regulation of hormone biosynthetic process | 12 | 3 |
| GO:BP | response to cadmium ion | 61 | 6 |
| GO:BP | regulation of localization | 2868 | 83 |
| GO:BP | C21-steroid hormone metabolic process | 42 | 5 |
| GO:BP | one-carbon metabolic process | 42 | 5 |
| GO:BP | isoprenoid metabolic process | 107 | 8 |
| GO:BP | renal system process involved in regulation of systemic arterial blood pressure | 26 | 4 |
| GO:BP | iron ion transport | 63 | 6 |
| GO:BP | regulation of lipid biosynthetic process | 187 | 11 |
| GO:BP | fructose metabolic process | 13 | 3 |
| GO:BP | dicarboxylic acid biosynthetic process | 13 | 3 |
| GO:BP | response to folic acid | 13 | 3 |
| GO:BP | alditol phosphate metabolic process | 13 | 3 |
| GO:BP | CDP-diacylglycerol metabolic process | 13 | 3 |
| GO:BP | positive regulation of nuclear-transcribed mRNA poly(A) tail shortening | 13 | 3 |
| GO:BP | positive regulation of protein exit from endoplasmic reticulum | 13 | 3 |
| GO:BP | formation of translation preinitiation complex | 13 | 3 |
| GO:BP | regulation of gluconeogenesis | 64 | 6 |
| GO:BP | regulation of blood coagulation | 64 | 6 |
| GO:BP | positive regulation of small molecule metabolic process | 161 | 10 |
| GO:BP | thyroid hormone metabolic process | 27 | 4 |
| GO:BP | cellular homeostasis | 956 | 34 |
| GO:BP | regulation of cell maturation | 27 | 4 |
| GO:BP | estrogen metabolic process | 27 | 4 |
| GO:BP | lipid modification | 218 | 12 |
| GO:BP | response to 2,3,7,8-tetrachlorodibenzodioxine | 4 | 2 |
| GO:BP | NADP biosynthetic process | 4 | 2 |
| GO:BP | porphyrin-containing compound catabolic process | 4 | 2 |
| GO:BP | heme catabolic process | 4 | 2 |
| GO:BP | multicellular organism development | 5441 | 142 |
| GO:BP | negative regulation of dendritic cell differentiation | 4 | 2 |
| GO:BP | endoplasmic reticulum tubular network membrane organization | 4 | 2 |
| GO:BP | L-kynurenine catabolic process | 4 | 2 |
| GO:BP | endoplasmic reticulum tubular network formation | 4 | 2 |
| GO:BP | pigment catabolic process | 4 | 2 |
| GO:BP | cellular response to peptide hormone stimulus | 309 | 15 |
| GO:BP | response to decreased oxygen levels | 341 | 16 |
| GO:BP | regulation of hemostasis | 66 | 6 |
| GO:BP | neuron death | 406 | 18 |
| GO:BP | positive regulation of fatty acid metabolic process | 46 | 5 |
| GO:BP | tetrapyrrole metabolic process | 46 | 5 |
| GO:BP | renal system process | 113 | 8 |
| GO:BP | carbohydrate derivative biosynthetic process | 574 | 23 |
| GO:BP | energy reserve metabolic process | 89 | 7 |
| GO:BP | growth hormone receptor signaling pathway | 14 | 3 |
| GO:BP | anatomical structure development | 5987 | 154 |
| GO:BP | regulation of nuclear-transcribed mRNA poly(A) tail shortening | 14 | 3 |
| GO:BP | aldehyde catabolic process | 14 | 3 |
| GO:BP | copper ion transport | 14 | 3 |
| GO:BP | regulation of coagulation | 67 | 6 |
| GO:BP | regulation of nitric oxide biosynthetic process | 67 | 6 |
| GO:BP | positive regulation of cell population proliferation | 1045 | 36 |
| GO:BP | sphingolipid metabolic process | 140 | 9 |
| GO:BP | heterocycle catabolic process | 410 | 18 |
| GO:BP | regulation of erythrocyte differentiation | 47 | 5 |
| GO:BP | response to lipoprotein particle | 29 | 4 |
| GO:BP | regulation of epidermal growth factor receptor signaling pathway | 68 | 6 |
| GO:BP | defense response | 1705 | 53 |
| GO:BP | regulation of nitric oxide metabolic process | 69 | 6 |
| GO:CC | cytoplasm | 11093 | 340 |
| GO:CC | organelle membrane | 3076 | 143 |
| GO:CC | endoplasmic reticulum | 1761 | 88 |
| GO:CC | endomembrane system | 4006 | 152 |
| GO:CC | endoplasmic reticulum membrane | 993 | 61 |
| GO:CC | endoplasmic reticulum subcompartment | 999 | 61 |
| GO:CC | nuclear outer membrane-endoplasmic reticulum membrane network | 1018 | 61 |
| GO:CC | intracellular anatomical structure | 14111 | 372 |
| GO:CC | organelle subcompartment | 1580 | 80 |
| GO:CC | mitochondrion | 1827 | 82 |
| GO:CC | envelope | 1176 | 61 |
| GO:CC | organelle envelope | 1176 | 61 |
| GO:CC | mitochondrial membrane | 677 | 43 |
| GO:CC | mitochondrial envelope | 736 | 44 |
| GO:CC | intracellular membrane-bounded organelle | 11363 | 307 |
| GO:CC | membrane-bounded organelle | 11812 | 312 |
| GO:CC | mitochondrial inner membrane | 451 | 30 |
| GO:CC | cellular anatomical entity | 19567 | 445 |
| GO:CC | apical plasma membrane | 388 | 26 |
| GO:CC | intracellular organelle | 12510 | 320 |
| GO:CC | apical part of cell | 474 | 29 |
| GO:CC | organelle inner membrane | 510 | 30 |
| GO:CC | organelle | 12827 | 324 |
| GO:CC | membrane | 10122 | 266 |
| GO:CC | cytosol | 3849 | 118 |
| GO:CC | lytic vacuole | 468 | 25 |
| GO:CC | lysosome | 468 | 25 |
| GO:CC | bounding membrane of organelle | 1676 | 61 |
| GO:CC | vacuole | 562 | 28 |
| GO:CC | basal part of cell | 291 | 18 |
| GO:CC | endosome membrane | 403 | 22 |
| GO:CC | peroxisome | 148 | 12 |
| GO:CC | microbody | 148 | 12 |
| GO:CC | basal plasma membrane | 272 | 17 |
| GO:CC | plasma membrane region | 1318 | 49 |
| GO:CC | vesicle | 2077 | 69 |
| GO:CC | Golgi apparatus | 1449 | 52 |
| GO:CC | vesicle membrane | 833 | 34 |
| GO:CC | cytoplasmic vesicle | 1931 | 64 |
| GO:CC | intracellular vesicle | 1937 | 64 |
| GO:CC | vacuolar membrane | 280 | 16 |
| GO:CC | endosome | 870 | 34 |
| GO:CC | brush border | 134 | 10 |
| GO:CC | basolateral plasma membrane | 239 | 14 |
| GO:CC | lytic vacuole membrane | 219 | 13 |
| GO:CC | lysosomal membrane | 219 | 13 |
| GO:CC | brush border membrane | 73 | 7 |
| GO:CC | Golgi apparatus subcompartment | 746 | 29 |
| GO:CC | azurophil granule | 12 | 3 |
| GO:CC | primary lysosome | 12 | 3 |
| GO:CC | microvillus | 106 | 8 |
| GO:CC | membrane raft | 392 | 18 |
| GO:CC | membrane microdomain | 393 | 18 |
| GO:MF | catalytic activity | 5665 | 223 |
| GO:MF | oxidoreductase activity | 815 | 63 |
| GO:MF | oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen | 217 | 22 |
| GO:MF | monooxygenase activity | 159 | 18 |
| GO:MF | small molecule binding | 2543 | 95 |
| GO:MF | anion binding | 2420 | 91 |
| GO:MF | vitamin binding | 141 | 16 |
| GO:MF | identical protein binding | 2140 | 82 |
| GO:MF | oxidoreductase activity, acting on CH-OH group of donors | 154 | 16 |
| GO:MF | iron ion binding | 211 | 18 |
| GO:MF | lyase activity | 198 | 17 |
| GO:MF | heme binding | 183 | 16 |
| GO:MF | pyridoxal phosphate binding | 54 | 9 |
| GO:MF | vitamin B6 binding | 55 | 9 |
| GO:MF | oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor | 143 | 14 |
| GO:MF | tetrapyrrole binding | 192 | 16 |
| GO:MF | ion binding | 5862 | 168 |
| GO:MF | transaminase activity | 22 | 6 |
| GO:MF | glutathione transferase activity | 33 | 7 |
| GO:MF | transferase activity, transferring nitrogenous groups | 23 | 6 |
| GO:MF | hydrolase activity | 2353 | 79 |
| GO:MF | acyltransferase activity, transferring groups other than amino-acyl groups | 232 | 16 |
| GO:MF | transferase activity | 2277 | 76 |
| GO:MF | acyltransferase activity | 263 | 17 |
| GO:MF | active transmembrane transporter activity | 346 | 20 |
| GO:MF | nucleoside phosphate binding | 2185 | 73 |
| GO:MF | nucleotide binding | 2185 | 73 |
| GO:MF | transferase activity, transferring alkyl or aryl (other than methyl) groups | 65 | 8 |
| GO:MF | transition metal ion binding | 1064 | 42 |
| GO:MF | nickel cation binding | 5 | 3 |
| GO:MF | aromatase activity | 36 | 6 |
| GO:MF | steroid hydroxylase activity | 69 | 8 |
| GO:MF | bile acid binding | 13 | 4 |
| GO:MF | monocarboxylic acid transmembrane transporter activity | 56 | 7 |
| GO:MF | transporter activity | 1137 | 43 |
| GO:MF | magnesium ion binding | 218 | 14 |
| GO:MF | lipid transporter activity | 147 | 11 |
| GO:MF | 1-acyl-2-lysophosphatidylserine acylhydrolase activity | 7 | 3 |
| GO:MF | phosphatidylserine 1-acylhydrolase activity | 7 | 3 |
| GO:MF | carboxylic acid binding | 174 | 12 |
| GO:MF | lipid binding | 786 | 32 |
| GO:MF | amide binding | 367 | 19 |
| GO:MF | N-acyltransferase activity | 103 | 9 |
| GO:MF | protein-containing complex binding | 1464 | 51 |
| GO:MF | carboxylic ester hydrolase activity | 153 | 11 |
| GO:MF | oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen | 65 | 7 |
| GO:MF | L-threonine ammonia-lyase activity | 2 | 2 |
| GO:MF | hormone binding | 85 | 8 |
| GO:MF | organic hydroxy compound transmembrane transporter activity | 47 | 6 |
| GO:MF | carboxylic acid transmembrane transporter activity | 155 | 11 |
| GO:MF | organic acid transmembrane transporter activity | 156 | 11 |
| GO:MF | flavin adenine dinucleotide binding | 90 | 8 |
| GO:MF | steroid binding | 114 | 9 |
| GO:MF | phospholipase A1 activity | 9 | 3 |
| GO:MF | peptide hormone binding | 51 | 6 |
| GO:MF | oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen | 54 | 6 |
| GO:MF | organic anion transmembrane transporter activity | 172 | 11 |
| GO:MF | triglyceride binding | 3 | 2 |
| GO:MF | peptidase regulator activity | 255 | 14 |
| GO:MF | long-chain fatty acid omega-hydroxylase activity | 3 | 2 |
| GO:MF | sphingolipid delta-4 desaturase activity | 3 | 2 |
| GO:MF | lipase activity | 124 | 9 |
| GO:MF | pattern recognition receptor activity | 23 | 4 |
| GO:MF | estrogen 2-hydroxylase activity | 3 | 2 |
| GO:MF | purine nucleobase binding | 3 | 2 |
| GO:MF | L-serine ammonia-lyase activity | 3 | 2 |
| GO:MF | bile acid transmembrane transporter activity | 23 | 4 |
| GO:MF | protein binding | 10189 | 248 |
| GO:MF | oxidoreductase activity, acting on paired donors, with oxidation of a pair of donors resulting in the reduction of molecular oxygen to two molecules of water | 11 | 3 |
| GO:MF | ATPase-coupled transmembrane transporter activity | 125 | 9 |
| GO:MF | monocarboxylic acid binding | 80 | 7 |
| GO:MF | primary active transmembrane transporter activity | 128 | 9 |
| GO:MF | carbon-sulfur lyase activity | 12 | 3 |
| GO:MF | triglyceride lipase activity | 42 | 5 |
| GO:MF | peptidase inhibitor activity | 214 | 12 |
| GO:MF | hydrolase activity, acting on ester bonds | 735 | 28 |
| GO:MF | acylglycerol lipase activity | 13 | 3 |
| GO:MF | carbon-nitrogen lyase activity | 13 | 3 |
| GO:MF | oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen | 27 | 4 |
| GO:MF | alcohol dehydrogenase (NADP+) activity | 27 | 4 |
| GO:MF | serine-type peptidase activity | 217 | 12 |
| GO:MF | sn-1-glycerol-3-phosphate C16:0-DCA-CoA acyl transferase activity | 4 | 2 |
| GO:MF | ferrous iron transmembrane transporter activity | 4 | 2 |
| GO:MF | N-acetyl-beta-D-galactosaminidase activity | 4 | 2 |
| GO:MF | thrombospondin receptor activity | 4 | 2 |
| GO:MF | glycerol-3-phosphate O-acyltransferase activity | 4 | 2 |
| GO:MF | oxidoreductase activity, acting on single donors with incorporation of molecular oxygen | 28 | 4 |
| GO:MF | folic acid binding | 14 | 3 |
| GO:MF | serine hydrolase activity | 222 | 12 |
| GO:MF | retinol binding | 14 | 3 |
| GO:MF | steroid dehydrogenase activity | 48 | 5 |
| GO:MF | aldo-keto reductase (NADP) activity | 30 | 4 |
| GO:MF | transmembrane transporter activity | 1053 | 36 |
| GO:MF | oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced iron-sulfur protein as one donor, and incorporation of one atom of oxygen | 15 | 3 |
| GO:MF | xenobiotic transmembrane transporter activity | 30 | 4 |
| GO:MF | estrogen receptor binding | 49 | 5 |
| GO:MF | peptide binding | 290 | 14 |
| GO:MF | organic acid binding | 145 | 9 |
| HP | Abnormal circulating metabolite concentration | 1099 | 64 |
| HP | Abnormal circulating carboxylic acid concentration | 216 | 23 |
| HP | Autosomal recessive inheritance | 2708 | 114 |
| HP | Abnormality of metabolism/homeostasis | 2240 | 96 |
| HP | Abnormal circulating amino acid concentration | 121 | 14 |
| HP | Abnormal urine metabolite level | 428 | 29 |
| KEGG | Metabolic pathways | 1563 | 110 |
| KEGG | Chemical carcinogenesis | 101 | 15 |
| KEGG | Bile secretion | 100 | 15 |
| KEGG | Biosynthesis of amino acids | 78 | 12 |
| KEGG | Cysteine and methionine metabolism | 52 | 9 |
| KEGG | Glutathione metabolism | 71 | 10 |
| KEGG | Drug metabolism - cytochrome P450 | 71 | 10 |
| KEGG | Metabolism of xenobiotics by cytochrome P450 | 73 | 10 |
| KEGG | Carbon metabolism | 121 | 13 |
| KEGG | Cholesterol metabolism | 49 | 8 |
| KEGG | Glycine, serine and threonine metabolism | 39 | 7 |
| KEGG | Lysosome | 131 | 13 |
| KEGG | Pyruvate metabolism | 44 | 7 |
| KEGG | Complement and coagulation cascades | 92 | 10 |
| KEGG | Glycerophospholipid metabolism | 98 | 10 |
| KEGG | Alanine, aspartate and glutamate metabolism | 38 | 6 |
| KEGG | Mineral absorption | 53 | 7 |
| KEGG | Tyrosine metabolism | 39 | 6 |
| KEGG | Steroid hormone biosynthesis | 91 | 9 |
| KEGG | Drug metabolism - other enzymes | 92 | 9 |
| KEGG | Glyoxylate and dicarboxylate metabolism | 31 | 5 |
| KEGG | Arginine biosynthesis | 20 | 4 |
| KEGG | Retinol metabolism | 97 | 9 |
| KEGG | Phenylalanine metabolism | 22 | 4 |
| REAC | Metabolism | 1679 | 118 |
| REAC | Metabolism of amino acids and derivatives | 234 | 29 |
| REAC | Metabolism of lipids | 573 | 40 |
| REAC | Biological oxidations | 204 | 19 |
| REAC | Phenylalanine and tyrosine metabolism | 10 | 4 |
| REAC | Bile acid and bile salt metabolism | 40 | 7 |
| REAC | Methylation | 12 | 4 |
| REAC | Recycling of bile acids and salts | 14 | 4 |
| REAC | Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol | 24 | 5 |
| REAC | Transport of small molecules | 635 | 35 |
| REAC | Metabolism of steroids | 112 | 11 |
| REAC | Heme degradation | 14 | 4 |
| REAC | Glutamate and glutamine metabolism | 13 | 4 |
| REAC | Pyruvate metabolism and Citric Acid (TCA) cycle | 50 | 7 |
| TF | Factor: GKLF; motif: NNNRGGNGNGGSN | 15302 | 377 |
| TF | Factor: Mxi1; motif: NCACGTGGSNGNNNN | 3073 | 104 |
| TF | Factor: GKLF; motif: NNNRGGNGNGGSN; match class: 1 | 10998 | 286 |
| TF | Factor: Egr-2; motif: GCGTGGGCGG | 7210 | 203 |
| TF | Factor: BCL6B; motif: NNNNCCGCCCCWNNNN | 13664 | 337 |
| TF | Factor: GKLF; motif: NNRRGRRNGNSNNN | 12950 | 322 |
| TF | Factor: ZFP187; motif: NNGMCCTNGTCCNYNN | 2555 | 87 |
| TF | Factor: ZBP89; motif: CCCCKCCCCCNN; match class: 1 | 3885 | 121 |
| TF | Factor: Pax-4; motif: NNNNNYCACCCB | 18716 | 428 |
| TF | Factor: Kid3; motif: CCACN; match class: 1 | 21165 | 462 |
| TF | Factor: Arnt; motif: NNNNNRTCACGTGAYNNNNN; match class: 1 | 7087 | 195 |
| TF | Factor: Arnt; motif: NNNNNRTCACGTGAYNNNNN | 7087 | 195 |
| TF | Factor: ZF5; motif: NRNGNGCGCGCWN | 14469 | 350 |
| TF | Factor: Sp1; motif: GGNGGGGGNGGGGGMGGGGCNGGG | 10752 | 274 |
| TF | Factor: ZBP89; motif: CCCCKCCCCCNN | 8105 | 217 |
| TF | Factor: Hes1; motif: NNCACGYGNN; match class: 1 | 11386 | 287 |
| TF | Factor: FOXN4; motif: NNWANNCGWMCGCGTCNNNNMT | 16009 | 378 |
| TF | Factor: E2F-1; motif: GNGGGCGGGRMN | 14228 | 344 |
| TF | Factor: FOXN4; motif: NNWANNCGWMCGCGTCNNNNMT; match class: 1 | 12768 | 315 |
| TF | Factor: c-Myc:Max; motif: NNACCACGTGGTNN; match class: 1 | 7970 | 213 |
| TF | Factor: c-Myc:Max; motif: NNACCACGTGGTNN | 7970 | 213 |
| TF | Factor: PPARgamma:RXR-alpha; motif: NTRGGNCARAGGKCA; match class: 1 | 5253 | 151 |
| TF | Factor: c-Myc:Max; motif: NNNNNNNCACGTGNNNNNNN; match class: 1 | 7236 | 196 |
| TF | Factor: c-Myc:Max; motif: NNNNNNNCACGTGNNNNNNN | 7236 | 196 |
| TF | Factor: WT1; motif: NNGGGNGGGSGN | 7486 | 201 |
| TF | Factor: WT1; motif: SMCNCCNSC | 8128 | 215 |
| TF | Factor: E2F-3; motif: GGCGGGN | 11268 | 282 |
| TF | Factor: PPAR,; motif: RGGNCAAAGGTCA | 2376 | 79 |
| TF | Factor: SP1:SP3; motif: CCSCCCCCYCC | 6684 | 182 |
| TF | Factor: USF2; motif: CASGYG | 6304 | 173 |
| TF | Factor: USF2; motif: CASGYG; match class: 1 | 6304 | 173 |
| TF | Factor: MAZ; motif: NKGGGAGGGGRGGR | 7957 | 210 |
| TF | Factor: ZF5; motif: GSGCGCGR | 14821 | 353 |
| TF | Factor: Klf15; motif: RGGGMGGRGNNGGGGGNGG | 3269 | 101 |
| TF | Factor: HIF-1alpha; motif: NCACGT | 6382 | 174 |
| TF | Factor: NF-E2; motif: CATGACTCAGCANNCN; match class: 1 | 47 | 7 |
| TF | Factor: CKROX; motif: SCCCTCCCC | 6334 | 173 |
| TF | Factor: E2F-4; motif: NTTTCSCGCC | 10545 | 265 |
| TF | Factor: ARNTLIKE; motif: NNNSCACGTG | 5261 | 148 |
| TF | Factor: MAZ; motif: GGGGAGGG | 8416 | 219 |
| TF | Factor: C-Myc; motif: NGCCACGTGNN | 6226 | 170 |
| TF | Factor: E2F-4; motif: NTTTCSCGCC; match class: 1 | 5364 | 150 |
| TF | Factor: ZF5; motif: GYCGCGCARNGCNN | 9484 | 241 |
| TF | Factor: CACD; motif: CCACRCCC | 10859 | 270 |
| TF | Factor: BEN; motif: CAGCGRNV | 16234 | 378 |
| TF | Factor: Zfp281; motif: NNCCCCCCCCCCMYC | 3971 | 116 |
| TF | Factor: E2F-4; motif: GCGGGAAANA | 10318 | 258 |
| TF | Factor: GKLF; motif: NNRRGRRNGNSNNN; match class: 1 | 8470 | 218 |
| TF | Factor: USF; motif: GYCACGTGNC | 3536 | 105 |
| TF | Factor: Sp1; motif: NNGGGGCGGGGNN | 8939 | 228 |
| TF | Factor: c-Myc; motif: KACCACGTGSYY | 5491 | 151 |
| TF | Factor: SP1:SP3; motif: CCSCCCCCYCC; match class: 1 | 3378 | 101 |
| TF | Factor: Osx; motif: CCNCCCCCNNN | 6158 | 166 |
| TF | Factor: ZF5; motif: GYCGCGCARNGCNN; match class: 1 | 5819 | 158 |
| TF | Factor: HNF4; motif: TGAMCTTTGNCCN | 2230 | 72 |
| TF | Factor: Pax-4; motif: NNNNNYCACCCB; match class: 1 | 14458 | 342 |
| TF | Factor: NGFI-C; motif: WTGCGTGGGYGG | 5000 | 139 |
| TF | Factor: VDR; motif: GGGKNARNRRGGWSA | 10051 | 251 |
| TF | Factor: E2F-4; motif: NGGGGGCGGGRMNN | 6987 | 184 |
| TF | Factor: MAZ; motif: NKGGGAGGGGRGGR; match class: 1 | 4159 | 119 |
| TF | Factor: E2F; motif: GGCGSG | 10391 | 258 |
| TF | Factor: Hes1; motif: NNCACGYGNN | 15504 | 362 |
| TF | Factor: BTEB2; motif: GNAGGGGGNGGGSSNN | 4977 | 138 |
| TF | Factor: TEL1; motif: CNCGGAANNN | 10420 | 258 |
| TF | Factor: HNF4alpha1; motif: NRGGNCAAAGGTCAN | 2111 | 68 |
| TF | Factor: Pax-5; motif: BCNNNRNGCANBGNTGNRTAGCSGCHNB; match class: 1 | 3991 | 114 |
| TF | Factor: Tcfl5; motif: NNCNCGNGNN; match class: 1 | 6337 | 168 |
| TF | Factor: STAT1; motif: NNNSANTTCCGGGAANTGNSN; match class: 1 | 2881 | 87 |
| TF | Factor: Tcfl5; motif: NNCNCGNGNN | 6337 | 168 |
| TF | Factor: VDR; motif: GGGKNARNRRGGWSA; match class: 1 | 3798 | 109 |
| TF | Factor: Clock; motif: CNGNCACGTGNNNM | 1665 | 56 |
| TF | Factor: Sp1; motif: GGGGCGGGGC | 8654 | 219 |
| TF | Factor: E2F-4; motif: GNNGGCGGGAAN | 5907 | 158 |
| TF | Factor: Myc; motif: CACGTGS | 5129 | 140 |
| TF | Factor: Sp1; motif: GGNGGGGGNGGGGGMGGGGCNGGG; match class: 1 | 7397 | 191 |
| TF | Factor: Sp5; motif: RNGGRGGNGGRGNNGGGGGAGGRG; match class: 1 | 1948 | 63 |
| TF | Factor: CREB,; motif: NTGACGTNA | 8122 | 207 |
| TF | Factor: AP-2beta; motif: GCNNNGGSCNGVGGGN | 5101 | 139 |
| TF | Factor: LKLF; motif: CNCCACCCS | 5803 | 155 |
| TF | Factor: ZF5; motif: GSGCGCGR; match class: 1 | 12032 | 290 |
| TF | Factor: AhR,; motif: NRCGTGNGN | 4421 | 123 |
| TF | Factor: Sp1; motif: NGGGGGCGGGGYN | 8784 | 221 |
| TF | Factor: NF-E2; motif: CATGACTCAGCANNCN | 1201 | 43 |
| TF | Factor: Max; motif: NMSCACGTGGC | 1243 | 44 |
| TF | Factor: Sp1; motif: NGGGGCGGGGN | 9122 | 228 |
| TF | Factor: Max; motif: NNANCACGTGNTNN | 7339 | 189 |
| TF | Factor: Max; motif: NNANCACGTGNTNN; match class: 1 | 7339 | 189 |
| TF | Factor: Sp1; motif: GGGGCGGGGT | 8345 | 211 |
| TF | Factor: CPBP; motif: SNCCCNN; match class: 1 | 19929 | 441 |
| TF | Factor: CP2/LBP-1c/LSF; motif: GCTGGNTNGNNCYNG; match class: 1 | 2369 | 73 |
| TF | Factor: N-Myc; motif: NNCCACGTGNNN | 4316 | 120 |
| TF | Factor: LKLF; motif: GGGGTGGKSN | 9186 | 229 |
| TF | Factor: SP4; motif: NNWAGGCGTGNCNNN | 4923 | 134 |
| TF | Factor: E2F-1; motif: GNGGGCGGGRMN; match class: 1 | 10601 | 259 |
| TF | Factor: WT1; motif: NNGGGNGGGSGN; match class: 1 | 3877 | 109 |
| TF | Factor: CTCF; motif: NAGGGGGCGCNNKNNNN | 14310 | 335 |
| TF | Factor: bach2; motif: TGCTGAGTCAY; match class: 1 | 21 | 4 |
| TF | Factor: AP-2alphaA; motif: ANNGCCTNAGGSNNT | 5089 | 137 |
| TF | Factor: MYB; motif: NNAACTGN | 1535 | 51 |
| TF | Factor: C-Myc; motif: NGCCACGTGNN; match class: 1 | 4317 | 119 |
| TF | Factor: Smad3; motif: NNCTSNCWSCWS | 10078 | 247 |
| TF | Factor: Sp5; motif: RNGGRGGNGGRGNNGGGGGAGGRG | 4848 | 131 |
| TF | Factor: SREBP-1; motif: CACSCCA; match class: 1 | 2459 | 74 |
| TF | Factor: Tax/CREB; motif: GGGGGTTGACGYANA | 5338 | 142 |
| TF | Factor: WT1; motif: NGCGGGGGGGTSMMCYN | 5297 | 141 |
| TF | Factor: Zic3; motif: NMCCCCCGGGGGGGN; match class: 1 | 2035 | 63 |
| TF | Factor: STAT3; motif: NNTCAYTTCCYGKNA; match class: 1 | 1373 | 46 |
| TF | Factor: SP2; motif: GNNGGGGGCGGGGSN | 7094 | 181 |
| TF | Factor: PPAR; motif: TGACCTTTGNCCY | 6027 | 157 |
| TF | Factor: SREBP-2; motif: NNGYCACNNSMN | 7690 | 194 |
| TF | Factor: E2F; motif: GGCGSG; match class: 1 | 7016 | 179 |
| TF | Factor: c-Myc:Max; motif: GCCAYGYGSN | 7338 | 186 |
| TF | Factor: c-Myc:Max; motif: GCCAYGYGSN; match class: 1 | 2409 | 72 |
| TF | Factor: Mycn; motif: NSCACGTGGC | 154 | 10 |
| TF | Factor: GKLF; motif: GCCMCRCCCNNN | 7840 | 197 |
| WP | Metapathway biotransformation | 141 | 16 |
| WP | One carbon metabolism and related pathways | 52 | 8 |
| WP | Oxidation by Cytochrome P450 | 40 | 7 |
| WP | Amino Acid metabolism | 95 | 11 |
| WP | Retinol metabolism | 39 | 7 |
2.2.6 Functional Enrichment - Liver TCDD-AhR Regulated
kable(Liver_Interx_PathwayEnrichment$result %>% dplyr::select(source, term_name, term_size, intersection_size),
table.attr = "class=\"striped\"", format = "html")| source | term_name | term_size | intersection_size |
|---|---|---|---|
| CORUM | Parvulin-associated pre-rRNP complex | 46 | 9 |
| GO:BP | cellular amide metabolic process | 1077 | 55 |
| GO:BP | cellular metabolic process | 10350 | 214 |
| GO:BP | small molecule metabolic process | 1713 | 69 |
| GO:BP | organonitrogen compound biosynthetic process | 1570 | 65 |
| GO:BP | organic acid metabolic process | 944 | 49 |
| GO:BP | metabolic process | 11429 | 226 |
| GO:BP | peptide metabolic process | 835 | 45 |
| GO:BP | carboxylic acid metabolic process | 896 | 46 |
| GO:BP | oxoacid metabolic process | 908 | 46 |
| GO:BP | obsolete oxidation-reduction process | 548 | 35 |
| GO:BP | organic substance metabolic process | 10989 | 214 |
| GO:BP | peptide biosynthetic process | 677 | 37 |
| GO:BP | monocarboxylic acid metabolic process | 616 | 35 |
| GO:BP | amide biosynthetic process | 793 | 40 |
| GO:BP | translation | 657 | 36 |
| GO:BP | organic acid biosynthetic process | 290 | 24 |
| GO:BP | catabolic process | 2399 | 75 |
| GO:BP | primary metabolic process | 10243 | 200 |
| GO:BP | organonitrogen compound metabolic process | 6326 | 142 |
| GO:BP | carboxylic acid biosynthetic process | 282 | 22 |
| GO:BP | cellular lipid metabolic process | 994 | 42 |
| GO:BP | organic substance catabolic process | 1985 | 64 |
| GO:BP | small molecule biosynthetic process | 617 | 32 |
| GO:BP | cellular catabolic process | 2059 | 65 |
| GO:BP | lipid metabolic process | 1344 | 48 |
| GO:BP | sulfur compound metabolic process | 317 | 21 |
| GO:BP | fatty acid metabolic process | 425 | 24 |
| GO:BP | regulation of biological quality | 3876 | 94 |
| GO:BP | ribonucleoprotein complex biogenesis | 413 | 23 |
| GO:BP | biosynthetic process | 5882 | 125 |
| GO:BP | cytoplasmic translation | 101 | 11 |
| GO:BP | ribosome assembly | 63 | 9 |
| GO:BP | organic substance biosynthetic process | 5779 | 121 |
| GO:BP | small molecule catabolic process | 346 | 19 |
| GO:BP | monocarboxylic acid biosynthetic process | 194 | 14 |
| GO:BP | ribosome biogenesis | 288 | 17 |
| GO:BP | nitrogen compound metabolic process | 9669 | 176 |
| GO:BP | ribonucleoprotein complex assembly | 182 | 13 |
| GO:BP | cellular biosynthetic process | 5715 | 117 |
| GO:BP | ribonucleoprotein complex subunit organization | 188 | 13 |
| GO:BP | toxin metabolic process | 17 | 5 |
| GO:BP | benzene-containing compound metabolic process | 30 | 6 |
| GO:BP | glutathione metabolic process | 70 | 8 |
| GO:BP | response to toxic substance | 240 | 14 |
| GO:BP | cellular modified amino acid metabolic process | 179 | 12 |
| GO:BP | organophosphate metabolic process | 891 | 30 |
| GO:BP | fatty acid biosynthetic process | 151 | 11 |
| GO:BP | gland development | 513 | 21 |
| GO:BP | NADP metabolic process | 38 | 6 |
| GO:BP | unsaturated fatty acid metabolic process | 133 | 10 |
| GO:BP | glycosyl compound metabolic process | 86 | 8 |
| GO:BP | liver development | 173 | 11 |
| GO:BP | response to xenobiotic stimulus | 115 | 9 |
| GO:BP | response to hormone | 912 | 29 |
| GO:BP | rRNA processing | 208 | 12 |
| GO:BP | protein metabolic process | 5474 | 108 |
| GO:BP | hepaticobiliary system development | 176 | 11 |
| GO:BP | xenobiotic catabolic process | 15 | 4 |
| GO:BP | cell redox homeostasis | 29 | 5 |
| GO:BP | ribosomal small subunit biogenesis | 69 | 7 |
| GO:BP | cellular lipid catabolic process | 214 | 12 |
| GO:BP | mature ribosome assembly | 6 | 3 |
| GO:BP | rRNA metabolic process | 217 | 12 |
| GO:BP | carboxylic acid catabolic process | 221 | 12 |
| GO:BP | organonitrogen compound catabolic process | 1249 | 35 |
| GO:BP | xenobiotic metabolic process | 102 | 8 |
| GO:BP | cellular protein metabolic process | 4815 | 96 |
| GO:BP | cellular response to chemical stimulus | 3097 | 68 |
| GO:BP | monoacylglycerol catabolic process | 7 | 3 |
| GO:BP | very long-chain fatty acid metabolic process | 33 | 5 |
| GO:BP | carbohydrate metabolic process | 587 | 21 |
| GO:BP | ketone catabolic process | 18 | 4 |
| GO:BP | organic acid catabolic process | 228 | 12 |
| GO:BP | nucleobase metabolic process | 34 | 5 |
| GO:BP | positive regulation of cellular amide metabolic process | 163 | 10 |
| GO:BP | regulation of angiogenesis | 305 | 14 |
| GO:BP | purine nucleobase metabolic process | 19 | 4 |
| GO:BP | cellular response to xenobiotic stimulus | 106 | 8 |
| GO:BP | positive regulation of translation | 135 | 9 |
| GO:BP | cellular nitrogen compound metabolic process | 6201 | 117 |
| GO:BP | carbohydrate derivative metabolic process | 975 | 29 |
| GO:BP | lipid biosynthetic process | 647 | 22 |
| GO:BP | blood vessel morphogenesis | 647 | 22 |
| GO:BP | homeostatic process | 1922 | 47 |
| GO:BP | alpha-amino acid catabolic process | 80 | 7 |
| GO:BP | regulation of vasculature development | 310 | 14 |
| GO:BP | cellular detoxification | 108 | 8 |
| GO:BP | response to oxygen-containing compound | 1820 | 45 |
| GO:BP | androgen biosynthetic process | 8 | 3 |
| GO:BP | ribosomal small subunit assembly | 20 | 4 |
| GO:BP | regulation of cellular amide metabolic process | 438 | 17 |
| GO:BP | cellular process | 17828 | 272 |
| GO:BP | cellular aldehyde metabolic process | 59 | 6 |
| GO:BP | response to insulin | 284 | 13 |
| GO:BP | nucleoside metabolic process | 61 | 6 |
| GO:BP | secondary metabolic process | 61 | 6 |
| GO:BP | NADPH oxidation | 9 | 3 |
| GO:BP | long-chain fatty acid metabolic process | 115 | 8 |
| GO:BP | cellular response to toxic substance | 115 | 8 |
| GO:BP | response to oxygen radical | 22 | 4 |
| GO:BP | response to superoxide | 22 | 4 |
| GO:BP | nucleobase-containing small molecule metabolic process | 537 | 19 |
| GO:BP | angiogenesis | 545 | 19 |
| GO:BP | liver regeneration | 42 | 5 |
| GO:BP | response to drug | 459 | 17 |
| GO:BP | animal organ regeneration | 91 | 7 |
| GO:BP | lipid catabolic process | 335 | 14 |
| GO:BP | negative regulation of cell adhesion mediated by integrin | 10 | 3 |
| GO:BP | positive regulation of establishment of protein localization to telomere | 10 | 3 |
| GO:BP | regulation of translation | 377 | 15 |
| GO:BP | cellular amino acid catabolic process | 92 | 7 |
| GO:BP | androgen metabolic process | 24 | 4 |
| GO:BP | membrane lipid metabolic process | 187 | 10 |
| GO:BP | detoxification | 123 | 8 |
| GO:BP | blood vessel development | 743 | 23 |
| GO:BP | drug metabolic process | 68 | 6 |
| GO:BP | localization | 6168 | 114 |
| GO:BP | regulation of establishment of protein localization to telomere | 11 | 3 |
| GO:BP | kynurenine metabolic process | 11 | 3 |
| GO:BP | ribosomal large subunit biogenesis | 69 | 6 |
| GO:BP | anatomical structure formation involved in morphogenesis | 1165 | 31 |
| GO:BP | tube morphogenesis | 911 | 26 |
| GO:BP | lactation | 72 | 6 |
| GO:BP | maturation of LSU-rRNA | 27 | 4 |
| GO:BP | estrogen metabolic process | 27 | 4 |
| GO:BP | regulation of establishment of protein localization to chromosome | 12 | 3 |
| GO:BP | response to organic substance | 3418 | 70 |
| GO:BP | regulation of endocannabinoid signaling pathway | 3 | 2 |
| GO:BP | positive regulation of cell cycle phase transition | 102 | 7 |
| GO:BP | positive regulation of DNA biosynthetic process | 74 | 6 |
| GO:BP | vasculature development | 773 | 23 |
| GO:BP | icosanoid metabolic process | 134 | 8 |
| GO:BP | response to oxidative stress | 447 | 16 |
| GO:BP | cellular hormone metabolic process | 135 | 8 |
| GO:BP | ncRNA processing | 363 | 14 |
| GO:BP | mammary gland development | 170 | 9 |
| GO:BP | positive regulation of protein localization to chromosome, telomeric region | 13 | 3 |
| GO:BP | monoacylglycerol metabolic process | 13 | 3 |
| GO:BP | response to peptide hormone | 452 | 16 |
| GO:BP | tube development | 1137 | 30 |
| GO:BP | cell death | 2136 | 48 |
| GO:BP | prostaglandin metabolic process | 52 | 5 |
| GO:BP | prostanoid metabolic process | 52 | 5 |
| GO:BP | organic cyclic compound catabolic process | 458 | 16 |
| GO:BP | sphingolipid metabolic process | 140 | 8 |
| GO:BP | parturition | 14 | 3 |
| GO:BP | aldehyde catabolic process | 14 | 3 |
| GO:BP | cellular ketone metabolic process | 213 | 10 |
| GO:BP | cellular amino acid metabolic process | 253 | 11 |
| GO:BP | response to inorganic substance | 604 | 19 |
| GO:BP | positive regulation of mitotic cell cycle phase transition | 81 | 6 |
| GO:BP | glutathione derivative metabolic process | 4 | 2 |
| GO:BP | regulation of complement activation | 15 | 3 |
| GO:BP | nitrobenzene metabolic process | 4 | 2 |
| GO:BP | protein localization to organelle | 859 | 24 |
| GO:BP | negative regulation of osteoblast differentiation | 56 | 5 |
| GO:BP | positive regulation of mitotic cell cycle | 114 | 7 |
| GO:BP | regulation of protein localization to chromosome, telomeric region | 15 | 3 |
| GO:BP | alpha-amino acid metabolic process | 182 | 9 |
| GO:BP | negative regulation of endothelial cell chemotaxis | 4 | 2 |
| GO:BP | L-kynurenine catabolic process | 4 | 2 |
| GO:BP | glutathione derivative biosynthetic process | 4 | 2 |
| GO:BP | response to copper ion | 33 | 4 |
| GO:BP | cellular response to insulin stimulus | 222 | 10 |
| GO:BP | nucleobase biosynthetic process | 16 | 3 |
| GO:BP | aromatic amino acid family catabolic process | 16 | 3 |
| GO:BP | ribosome localization | 16 | 3 |
| GO:BP | formation of cytoplasmic translation initiation complex | 16 | 3 |
| GO:BP | establishment of protein localization to telomere | 16 | 3 |
| GO:BP | establishment of localization | 4658 | 88 |
| GO:BP | ribosomal subunit export from nucleus | 16 | 3 |
| GO:BP | reactive oxygen species metabolic process | 225 | 10 |
| GO:BP | steroid metabolic process | 306 | 12 |
| GO:BP | cytoplasmic translational initiation | 35 | 4 |
| GO:BP | response to peptide | 531 | 17 |
| GO:BP | programmed cell death | 1975 | 44 |
| GO:BP | cellular response to peptide hormone stimulus | 309 | 12 |
| GO:BP | apoptotic process | 1919 | 43 |
| GO:BP | cellular response to vascular endothelial growth factor stimulus | 60 | 5 |
| GO:BP | system development | 4876 | 91 |
| GO:BP | rRNA-containing ribonucleoprotein complex export from nucleus | 17 | 3 |
| GO:BP | glutamine family amino acid biosynthetic process | 17 | 3 |
| GO:BP | translational initiation | 121 | 7 |
| GO:BP | response to organic cyclic compound | 1043 | 27 |
| GO:BP | body fluid secretion | 123 | 7 |
| GO:BP | alpha-amino acid biosynthetic process | 62 | 5 |
| GO:BP | cellular amino acid biosynthetic process | 62 | 5 |
| GO:BP | ncRNA metabolic process | 449 | 15 |
| GO:BP | activation of membrane attack complex | 5 | 2 |
| GO:BP | arginine biosynthetic process | 5 | 2 |
| GO:BP | iron ion transport | 63 | 5 |
| GO:BP | viral translational termination-reinitiation | 5 | 2 |
| GO:BP | fatty acid beta-oxidation using acyl-CoA oxidase | 5 | 2 |
| GO:BP | removal of superoxide radicals | 18 | 3 |
| GO:BP | protein sulfation | 5 | 2 |
| GO:CC | cytoplasm | 11093 | 242 |
| GO:CC | intracellular anatomical structure | 14111 | 262 |
| GO:CC | cytosolic ribosome | 112 | 19 |
| GO:CC | ribosome | 236 | 25 |
| GO:CC | ribosomal subunit | 200 | 23 |
| GO:CC | cytosol | 3849 | 110 |
| GO:CC | intracellular organelle | 12510 | 234 |
| GO:CC | organelle | 12827 | 235 |
| GO:CC | small ribosomal subunit | 79 | 13 |
| GO:CC | intracellular membrane-bounded organelle | 11363 | 214 |
| GO:CC | cytosolic small ribosomal subunit | 45 | 10 |
| GO:CC | membrane-bounded organelle | 11812 | 215 |
| GO:CC | ribonucleoprotein complex | 725 | 32 |
| GO:CC | endomembrane system | 4006 | 96 |
| GO:CC | endoplasmic reticulum | 1761 | 54 |
| GO:CC | cytosolic large ribosomal subunit | 64 | 9 |
| GO:CC | mitochondrion | 1827 | 52 |
| GO:CC | organelle membrane | 3076 | 75 |
| GO:CC | large ribosomal subunit | 126 | 11 |
| GO:CC | organelle subcompartment | 1580 | 46 |
| GO:CC | polysomal ribosome | 32 | 6 |
| GO:CC | endoplasmic reticulum membrane | 993 | 32 |
| GO:CC | endoplasmic reticulum subcompartment | 999 | 32 |
| GO:CC | nuclear outer membrane-endoplasmic reticulum membrane network | 1018 | 32 |
| GO:CC | polysome | 70 | 7 |
| GO:CC | mitochondrial envelope | 736 | 24 |
| GO:CC | organelle envelope | 1176 | 33 |
| GO:CC | envelope | 1176 | 33 |
| GO:CC | chaperonin-containing T-complex | 10 | 3 |
| GO:CC | mitochondrial intermembrane space | 99 | 7 |
| GO:CC | myelin sheath | 206 | 10 |
| GO:CC | rough endoplasmic reticulum | 105 | 7 |
| GO:CC | mitochondrial inner membrane | 451 | 16 |
| GO:CC | synapse | 1467 | 36 |
| GO:CC | organelle envelope lumen | 111 | 7 |
| GO:CC | eukaryotic 48S preinitiation complex | 15 | 3 |
| GO:CC | COP9 signalosome | 34 | 4 |
| GO:CC | eukaryotic translation initiation factor 3 complex | 16 | 3 |
| GO:CC | mitochondrial membrane | 677 | 20 |
| GO:CC | eukaryotic 43S preinitiation complex | 17 | 3 |
| GO:CC | translation preinitiation complex | 18 | 3 |
| GO:CC | organelle inner membrane | 510 | 16 |
| GO:CC | cellular anatomical entity | 19567 | 288 |
| GO:CC | membrane-enclosed lumen | 4582 | 85 |
| GO:CC | intracellular organelle lumen | 4581 | 85 |
| GO:CC | organelle lumen | 4582 | 85 |
| GO:CC | preribosome | 74 | 5 |
| GO:CC | intracellular non-membrane-bounded organelle | 4500 | 83 |
| GO:CC | preribosome, large subunit precursor | 24 | 3 |
| GO:CC | non-membrane-bounded organelle | 4515 | 83 |
| GO:CC | microbody | 148 | 7 |
| GO:CC | peroxisome | 148 | 7 |
| GO:MF | oxidoreductase activity | 815 | 43 |
| GO:MF | structural constituent of ribosome | 172 | 21 |
| GO:MF | rRNA binding | 69 | 12 |
| GO:MF | catalytic activity | 5665 | 129 |
| GO:MF | oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor | 143 | 13 |
| GO:MF | oxidoreductase activity, acting on CH-OH group of donors | 154 | 13 |
| GO:MF | flavin adenine dinucleotide binding | 90 | 10 |
| GO:MF | structural molecule activity | 612 | 25 |
| GO:MF | identical protein binding | 2140 | 54 |
| GO:MF | lyase activity | 198 | 12 |
| GO:MF | translation regulator activity | 145 | 10 |
| GO:MF | anion binding | 2420 | 58 |
| GO:MF | RNA binding | 1267 | 36 |
| GO:MF | oligopeptide binding | 17 | 4 |
| GO:MF | glutathione binding | 17 | 4 |
| GO:MF | small molecule binding | 2543 | 59 |
| GO:MF | oxidoreductase activity, acting on a sulfur group of donors | 51 | 6 |
| GO:MF | carbonyl reductase (NADPH) activity | 7 | 3 |
| GO:MF | NADP binding | 55 | 6 |
| GO:MF | enzyme inhibitor activity | 403 | 16 |
| GO:MF | oxidoreductase activity, acting on the CH-CH group of donors | 60 | 6 |
| GO:MF | N,N-dimethylaniline monooxygenase activity | 9 | 3 |
| GO:MF | ubiquitin ligase inhibitor activity | 9 | 3 |
| GO:MF | site-specific endodeoxyribonuclease activity, specific for altered base | 2 | 2 |
| GO:MF | transition metal ion binding | 1064 | 30 |
| GO:MF | amino acid binding | 63 | 6 |
| GO:MF | ubiquitin-protein transferase inhibitor activity | 10 | 3 |
| GO:MF | carboxylic ester hydrolase activity | 153 | 9 |
| GO:MF | ion binding | 5862 | 110 |
| GO:MF | mRNA 5’-UTR binding | 25 | 4 |
| GO:MF | protein-disulfide reductase activity | 27 | 4 |
| GO:MF | 5.8S rRNA binding | 3 | 2 |
| GO:MF | carbon-sulfur lyase activity | 12 | 3 |
| GO:MF | palmitoyl-CoA oxidase activity | 3 | 2 |
| GO:MF | 5S rRNA binding | 13 | 3 |
| GO:MF | acylglycerol lipase activity | 13 | 3 |
| GO:MF | nucleoside phosphate binding | 2185 | 49 |
| GO:MF | nucleotide binding | 2185 | 49 |
| GO:MF | translation regulator activity, nucleic acid binding | 113 | 7 |
| GO:MF | glutathione transferase activity | 33 | 4 |
| GO:MF | 3-hydroxy-lignoceroyl-CoA dehydratase activity | 4 | 2 |
| GO:MF | very-long-chain 3-hydroxyacyl-CoA dehydratase activity | 4 | 2 |
| GO:MF | 3-hydroxy-arachidoyl-CoA dehydratase activity | 4 | 2 |
| GO:MF | 3-hydroxy-behenoyl-CoA dehydratase activity | 4 | 2 |
| GO:MF | oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen | 217 | 10 |
| GO:MF | steroid binding | 114 | 7 |
| GO:MF | disulfide oxidoreductase activity | 34 | 4 |
| GO:MF | protein folding chaperone | 35 | 4 |
| GO:MF | hydro-lyase activity | 61 | 5 |
| GO:MF | organic cyclic compound binding | 5768 | 105 |
| GO:MF | oxidoreductase activity, acting on superoxide radicals as acceptor | 5 | 2 |
| GO:MF | NAD binding | 63 | 5 |
| GO:MF | lipase activity | 124 | 7 |
| GO:MF | superoxide dismutase activity | 5 | 2 |
| GO:MF | stearoyl-CoA 9-desaturase activity | 5 | 2 |
| GO:MF | monooxygenase activity | 159 | 8 |
| GO:MF | FAD binding | 39 | 4 |
| GO:MF | transferase activity, transferring alkyl or aryl (other than methyl) groups | 65 | 5 |
| GO:MF | translation factor activity, RNA binding | 96 | 6 |
| GO:MF | complement binding | 20 | 3 |
| GO:MF | acyl-CoA oxidase activity | 6 | 2 |
| GO:MF | metal cluster binding | 71 | 5 |
| GO:MF | iron-sulfur cluster binding | 71 | 5 |
| GO:MF | ubiquitin-protein transferase regulator activity | 22 | 3 |
| GO:MF | metalloaminopeptidase activity | 22 | 3 |
| HP | Abnormality of metabolism/homeostasis | 2240 | 65 |
| KEGG | Ribosome | 169 | 21 |
| KEGG | Metabolic pathways | 1563 | 64 |
| KEGG | Coronavirus disease - COVID-19 | 241 | 22 |
| KEGG | Biosynthesis of unsaturated fatty acids | 34 | 7 |
| KEGG | Metabolism of xenobiotics by cytochrome P450 | 73 | 9 |
| KEGG | Fatty acid elongation | 29 | 6 |
| KEGG | Drug metabolism - cytochrome P450 | 71 | 8 |
| KEGG | Drug metabolism - other enzymes | 92 | 9 |
| KEGG | Biosynthesis of amino acids | 78 | 8 |
| KEGG | Chemical carcinogenesis | 101 | 9 |
| KEGG | Glutathione metabolism | 71 | 7 |
| KEGG | Tryptophan metabolism | 51 | 6 |
| KEGG | Biosynthesis of cofactors | 154 | 10 |
| KEGG | Fatty acid metabolism | 62 | 6 |
| KEGG | Ovarian steroidogenesis | 62 | 6 |
| REAC | Formation of a pool of free 40S subunits | 98 | 20 |
| REAC | Metabolism | 1679 | 81 |
| REAC | GTP hydrolysis and joining of the 60S ribosomal subunit | 109 | 20 |
| REAC | L13a-mediated translational silencing of Ceruloplasmin expression | 108 | 20 |
| REAC | Eukaryotic Translation Initiation | 116 | 20 |
| REAC | Cap-dependent Translation Initiation | 116 | 20 |
| REAC | SRP-dependent cotranslational protein targeting to membrane | 89 | 17 |
| REAC | Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) | 91 | 17 |
| REAC | Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) | 110 | 17 |
| REAC | Nonsense-Mediated Decay (NMD) | 110 | 17 |
| REAC | Translation | 217 | 23 |
| REAC | Formation of the ternary complex, and subsequently, the 43S complex | 49 | 12 |
| REAC | Ribosomal scanning and start codon recognition | 56 | 12 |
| REAC | Translation initiation complex formation | 56 | 12 |
| REAC | Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S | 57 | 12 |
| REAC | rRNA processing | 167 | 18 |
| REAC | Major pathway of rRNA processing in the nucleolus and cytosol | 167 | 18 |
| REAC | rRNA processing in the nucleus and cytosol | 167 | 18 |
| REAC | Biological oxidations | 204 | 18 |
| REAC | FMO oxidises nucleophiles | 3 | 3 |
| REAC | Metabolism of lipids | 573 | 29 |
| REAC | Phase II - Conjugation of compounds | 91 | 10 |
| REAC | Fatty acid metabolism | 169 | 13 |
| REAC | Glutathione conjugation | 34 | 6 |
| REAC | Synthesis of (16-20)-hydroxyeicosatetraenoic acids (HETE) | 8 | 3 |
| REAC | Formation of the active cofactor, UDP-glucuronate | 3 | 2 |
| REAC | alpha-linolenic acid (ALA) metabolism | 12 | 3 |
| REAC | alpha-linolenic (omega3) and linoleic (omega6) acid metabolism | 12 | 3 |
| REAC | Phase I - Functionalization of compounds | 107 | 8 |
| TF | Factor: Kaiso; motif: SARNYCTCGCGAGAN; match class: 1 | 9949 | 201 |
| TF | Factor: E2F-1; motif: GNGGGCGGGRMN | 14228 | 254 |
| TF | Factor: ZF5; motif: GSGCGCGR | 14821 | 258 |
| TF | Factor: FOXN4; motif: NNWANNCGWMCGCGTCNNNNMT; match class: 1 | 12768 | 233 |
| TF | Factor: AhR; motif: NTNGCGTGNNN | 3488 | 93 |
| TF | Factor: ELK-1; motif: ACCGGAWRTN | 14697 | 255 |
| TF | Factor: E2F-4; motif: NTTTCSCGCC | 10545 | 202 |
| TF | Factor: FOXN4; motif: NNWANNCGWMCGCGTCNNNNMT | 16009 | 269 |
| TF | Factor: LKLF; motif: NGGGCGG | 7220 | 153 |
| TF | Factor: Sp3; motif: AGGGCGG | 7220 | 153 |
| TF | Factor: SP6; motif: WGGGCGG | 7220 | 153 |
| TF | Factor: CPBP; motif: NGGGCGG | 7220 | 153 |
| TF | Factor: ZF5; motif: NRNGNGCGCGCWN | 14469 | 250 |
| TF | Factor: E2F; motif: GGCGSG | 10391 | 196 |
| TF | Factor: ZF5; motif: NRNGNGCGCGCWN; match class: 1 | 11181 | 206 |
| TF | Factor: AhR:Arnt; motif: KNNKNNTYGCGTGCMS | 2875 | 77 |
| TF | Factor: ZF5; motif: GSGCGCGR; match class: 1 | 12032 | 216 |
| TF | Factor: BEN; motif: CAGCGRNV; match class: 1 | 11980 | 215 |
| TF | Factor: Kaiso; motif: SARNYCTCGCGAGAN | 13491 | 234 |
| TF | Factor: E2F-1; motif: GNGGGCGGGRMN; match class: 1 | 10601 | 196 |
| TF | Factor: Elk-1; motif: NNNNCCGGAARTNN | 10072 | 188 |
| TF | Factor: Hes1; motif: NNCACGYGNN; match class: 1 | 11386 | 206 |
| TF | Factor: E2F-1; motif: NNNSSCGCSAANN | 9013 | 173 |
| TF | Factor: Hes1; motif: NNCACGYGNN | 15504 | 257 |
| TF | Factor: Klf17; motif: NGGGCGG | 6533 | 135 |
| TF | Factor: AhR,; motif: NRCGTGNGN | 4421 | 100 |
| TF | Factor: PEA3; motif: RCCGGAAGYN | 9964 | 184 |
| TF | Factor: ZF5; motif: GYCGCGCARNGCNN | 9484 | 177 |
| TF | Factor: AhR; motif: CCYCNRRSTNGCGTGASA | 3480 | 82 |
| TF | Factor: SP100; motif: NNCGTCGNNTAAWNN | 8478 | 159 |
| TF | Factor: E2F; motif: NCSCGCSAAAN | 5198 | 109 |
| TF | Factor: E2F-4; motif: GNNGGCGGGAAN | 5907 | 120 |
| TF | Factor: AHR; motif: CACGCN; match class: 1 | 2729 | 67 |
| TF | Factor: IRF6; motif: NNNACTCYCGGKNNN | 13409 | 225 |
| TF | Factor: E2F-7; motif: GRGGCGGGAANNN | 7914 | 149 |
| TF | Factor: MYF6; motif: NNNRACAGNCNCNCC; match class: 1 | 7012 | 135 |
| TF | Factor: E2F; motif: TTTSGCGSG | 5455 | 111 |
| TF | Factor: GABP-alpha; motif: CTTCCK | 10764 | 189 |
| TF | Factor: E2F-3; motif: GGCGGGN | 11268 | 195 |
| TF | Factor: E2F1; motif: NNNNNGCGSSAAAN | 5835 | 116 |
| TF | Factor: SP6; motif: WGGGCGG; match class: 1 | 2360 | 58 |
| TF | Factor: CPBP; motif: NGGGCGG; match class: 1 | 2360 | 58 |
| TF | Factor: LKLF; motif: NGGGCGG; match class: 1 | 2360 | 58 |
| TF | Factor: Sp3; motif: AGGGCGG; match class: 1 | 2360 | 58 |
| TF | Factor: ELK-1; motif: ACCGGAWRTN; match class: 1 | 9029 | 163 |
| TF | Factor: MYF6; motif: NNNRACAGNCNCNCC | 14294 | 234 |
| TF | Factor: TEL1; motif: CNCGGAANNN | 10420 | 182 |
| TF | Factor: BEN; motif: CWGCGAYA | 6569 | 126 |
| TF | Factor: IRF4; motif: NNNAYTCTCGGWNNN; match class: 1 | 8126 | 149 |
| TF | Factor: AhR:Arnt; motif: GRGKATYGCGTGMCWNSCC | 5815 | 114 |
| TF | Factor: ZF5; motif: GYCGCGCARNGCNN; match class: 1 | 5819 | 114 |
| TF | Factor: Egr-2; motif: GCGTGGGCGG | 7210 | 135 |
| TF | Factor: BEN; motif: CAGCGRNV | 16234 | 257 |
| TF | Factor: E2F-1; motif: TTTSGCGS | 5974 | 116 |
| TF | Factor: AhR; motif: NTNGCGTGNNN; match class: 1 | 393 | 17 |
| TF | Factor: Pax-5; motif: RRMSWGANWYCTNRAGCGKRACSRYNSM | 11986 | 202 |
| TF | Factor: RNF96; motif: BCCCGCRGCC | 6337 | 121 |
| TF | Factor: c-Myc:Max; motif: GCCAYGYGSN; match class: 1 | 2409 | 57 |
| TF | Factor: Pax-3; motif: NNNNNNCGTCACGSTYNNNNN | 12917 | 214 |
| TF | Factor: HES-1; motif: GSCACGMGMC | 3590 | 77 |
| TF | Factor: E2F-1; motif: NTTSGCGG; match class: 1 | 1815 | 46 |
| TF | Factor: p53; motif: RGRCWWGYCYNGRCWWGYYY | 7799 | 142 |
| TF | Factor: ERG; motif: ACCGGAART | 9550 | 167 |
| TF | Factor: E2F-1; motif: TTTSGCGCGMNR | 5994 | 114 |
| TF | Factor: ZBED6; motif: NRRGCTCGCCNN | 5544 | 107 |
| TF | Factor: AhR; motif: NNNKNGCGTGNSNNNNN | 1222 | 34 |
| TF | Factor: SP4; motif: NNWAGGCGTGNCNNN | 4923 | 97 |
| TF | Factor: E2F; motif: NKCGCGCSAAAN | 4858 | 96 |
| TF | Factor: BCL6B; motif: NNNNCCGCCCCWNNNN | 13664 | 222 |
| TF | Factor: Pax-5; motif: RRMSWGANWYCTNRAGCGKRACSRYNSM; match class: 1 | 5518 | 106 |
| TF | Factor: SP4; motif: NNKGGGCGKGNCN | 1941 | 47 |
| TF | Factor: Ets2; motif: ACCGGAWRYN | 7919 | 142 |
| TF | Factor: TEL1; motif: CNCGGAANNN; match class: 1 | 4384 | 88 |
| TF | Factor: E2F-4; motif: GCGGGAAANA | 10318 | 176 |
| TF | Factor: E2F; motif: NNTTTCGCGCN | 5159 | 100 |
| TF | Factor: Tcfl5; motif: NNCNCGNGNN | 6337 | 118 |
| TF | Factor: Tcfl5; motif: NNCNCGNGNN; match class: 1 | 6337 | 118 |
| TF | Factor: SP1:SP3; motif: CCSCCCCCYCC | 6684 | 123 |
| TF | Factor: NGFI-C; motif: WTGCGTGGGYGG | 5000 | 97 |
| TF | Factor: c-ets-1; motif: ACCGGAWRYN | 8408 | 148 |
| TF | Factor: HIC1; motif: NNNGGKTGCCCSNNNNNN | 2851 | 62 |
| TF | Factor: HIF-1alpha; motif: NCACGT | 6382 | 118 |
| TF | Factor: Zic1; motif: NNCCCCCGGGGGGG | 9522 | 164 |
| TF | Factor: IRF4; motif: NNNAYTCTCGGWNNN | 14544 | 232 |
| TF | Factor: EGR-1; motif: TGCGTGGGCGK | 4136 | 83 |
| TF | Factor: CTCF; motif: NAGGGGGCGCNNKNNNN; match class: 1 | 9341 | 161 |
| TF | Factor: Elf-1; motif: AWCCCGGAAGTN | 8375 | 147 |
| TF | Factor: AhR; motif: CCYCNRRSTNGCGTGASA; match class: 1 | 383 | 15 |
| TF | Factor: c-Ets-1; motif: NNNRCCGGAWRYNNNN | 7309 | 131 |
| TF | Factor: E2F-1; motif: TTTSGCGS; match class: 1 | 1582 | 39 |
| TF | Factor: E2F-4; motif: NGGGGGCGGGRMNN | 6987 | 126 |
| TF | Factor: Egr-3; motif: NTGCGTGGGCGK | 6055 | 112 |
| TF | Factor: arnt; motif: CACGYA | 4582 | 89 |
| TF | Factor: SP2; motif: GGGCGGGAC | 8107 | 142 |
| TF | Factor: GKLF; motif: WGGGYGKGGCCN; match class: 1 | 3595 | 73 |
| TF | Factor: HIF-1alpha; motif: GNACGTGM | 6619 | 120 |
| TF | Factor: SP2; motif: GGGCGGGAC; match class: 1 | 3289 | 68 |
| TF | Factor: GKLF; motif: GCCMCRCCCNNN | 7840 | 138 |
| TF | Factor: AP-2alpha; motif: NGCCYSNNGSN | 6174 | 113 |
| TF | Factor: ELF4; motif: CCCGGAARTN | 7185 | 128 |
| TF | Factor: GKLF; motif: WGGGYGKGGCCN | 8978 | 154 |
| TF | Factor: HES-1; motif: NNCKYGTGNNN | 4062 | 80 |
| TF | Factor: E2F-1; motif: NNNSSCGCSAANN; match class: 1 | 4125 | 81 |
| TF | Factor: Sp1; motif: GGNGGGGGNGGGGGMGGGGCNGGG | 10752 | 179 |
| TF | Factor: Sp1; motif: NGGGGCGGGGN | 9122 | 156 |
| TF | Factor: E2F-4; motif: GCGGGAAANA; match class: 1 | 4700 | 90 |
| TF | Factor: Kid3; motif: CCACN; match class: 1 | 21165 | 305 |
| TF | Factor: CPBP; motif: SNCCCNN; match class: 1 | 19929 | 294 |
| TF | Factor: AP-2; motif: SNNNCCNCAGGCN | 7085 | 126 |
| TF | Factor: ZBED6; motif: NRRGCTCGCCNN; match class: 1 | 1364 | 34 |
| TF | Factor: ctcf; motif: CCNCNAGRKGGCRSTN | 5575 | 103 |
| TF | Factor: Erm; motif: NCCGGAWGTN | 5268 | 98 |
| TF | Factor: SP100; motif: NNCGTCGNNTAAWNN; match class: 1 | 3060 | 63 |
| TF | Factor: c-Myc:Max; motif: GCCAYGYGSN | 7338 | 129 |
| TF | Factor: MAF; motif: GCTGAGTCAN | 6937 | 123 |
| TF | Factor: AP-2; motif: MKCCCSCNGGCG | 8029 | 139 |
| TF | Factor: E2F-3; motif: GGCGGGN; match class: 1 | 6875 | 122 |
| TF | Factor: ER71; motif: ACCGGAARYN | 4325 | 83 |
| TF | Factor: Egr-2; motif: NTGCGTRGGCGK | 5359 | 99 |
| TF | Factor: AP-2beta; motif: GCNNNGGSCNGVGGGN | 5101 | 95 |
| TF | Factor: E2F-4; motif: NTTTCSCGCC; match class: 1 | 5364 | 99 |
| TF | Factor: AHR; motif: CACGCN | 8469 | 145 |
| TF | Factor: AP-2gamma; motif: GCCYNCRGSN | 7106 | 125 |
| TF | Factor: Zscan2; motif: GTCAAAACGC | 59 | 5 |
| TF | Factor: E2F; motif: TTTSGCGSG | 4808 | 90 |
| TF | Factor: BTEB2; motif: RGGGNGKGGN | 7600 | 132 |
| TF | Factor: GKLF; motif: NNNRGGNGNGGSN | 15302 | 238 |
| TF | Factor: Pet-1; motif: GCNGGAAGYG | 13321 | 212 |
| TF | Factor: IRF6; motif: NNNACTCYCGGKNNN; match class: 1 | 7128 | 125 |
| TF | Factor: SAP-1a; motif: NRRCCGGAAGYRN | 9134 | 154 |
| TF | Factor: Kaiso; motif: GCMGGGRGCRGS | 11131 | 182 |
| TF | Factor: REST; motif: KTCAGCACCAYGGACAGCKCCN | 7904 | 136 |
| TF | Factor: E2F-1; motif: NKTSSCGC | 7904 | 136 |
| TF | Factor: Elk-1; motif: NCCGGAAGTGN | 14565 | 228 |
| TF | Factor: Egr-2; motif: GCGTGGGCGG; match class: 1 | 2774 | 57 |
| TF | Factor: WT1; motif: SMCNCCNSC | 8128 | 139 |
| TF | Factor: GABPalpha_GABPbeta; motif: CTTCCKGY | 2969 | 60 |
| TF | Factor: Pax-3; motif: NNNNNNCGTCACGSTYNNNNN; match class: 1 | 6178 | 110 |
| TF | Factor: GKLF; motif: GCCMCRCCCNNN; match class: 1 | 2968 | 60 |
| TF | Factor: LRH-1; motif: NYCAAGGYCAN; match class: 1 | 411 | 14 |
| WP | Cytoplasmic Ribosomal Proteins | 81 | 17 |
| WP | Metapathway biotransformation | 141 | 12 |
| WP | Estrogen metabolism | 14 | 4 |
| WP | Omega-3/Omega-6 FA synthesis | 15 | 4 |
| WP | Translation Factors | 49 | 6 |
| WP | Selenium Micronutrient Network | 23 | 4 |
| WP | Folic Acid Network | 23 | 4 |
| WP | Oxidative Stress and Redox Pathway | 93 | 8 |
| WP | Tryptophan metabolism | 44 | 5 |
| WP | Omega-9 FA synthesis | 14 | 3 |
| WP | Oxidative Stress | 28 | 4 |
2.2.7 Functional Enrichment - Kidney Ahr Regulated
kable(Kidney_Ahr_PathwayEnrichment$result %>% dplyr::select(source, term_name, term_size, intersection_size),
table.attr = "class=\"striped\"", format = "html")| source | term_name | term_size | intersection_size |
|---|---|---|---|
| CORUM | Parvulin-associated pre-rRNP complex | 46 | 7 |
| GO:BP | small molecule metabolic process | 1713 | 82 |
| GO:BP | organic acid metabolic process | 944 | 53 |
| GO:BP | oxoacid metabolic process | 908 | 51 |
| GO:BP | carboxylic acid metabolic process | 896 | 50 |
| GO:BP | cellular amino acid metabolic process | 253 | 24 |
| GO:BP | alpha-amino acid metabolic process | 182 | 20 |
| GO:BP | cellular amide metabolic process | 1077 | 47 |
| GO:BP | organonitrogen compound biosynthetic process | 1570 | 58 |
| GO:BP | organonitrogen compound metabolic process | 6326 | 142 |
| GO:BP | lipid metabolic process | 1344 | 51 |
| GO:BP | small molecule catabolic process | 346 | 24 |
| GO:BP | metabolic process | 11429 | 211 |
| GO:BP | catabolic process | 2399 | 72 |
| GO:BP | organic substance catabolic process | 1985 | 63 |
| GO:BP | organic substance metabolic process | 10989 | 204 |
| GO:BP | small molecule biosynthetic process | 617 | 31 |
| GO:BP | obsolete oxidation-reduction process | 548 | 29 |
| GO:BP | cellular metabolic process | 10350 | 194 |
| GO:BP | carboxylic acid catabolic process | 221 | 18 |
| GO:BP | organic acid catabolic process | 228 | 18 |
| GO:BP | anion transport | 529 | 27 |
| GO:BP | monocarboxylic acid metabolic process | 616 | 29 |
| GO:BP | organic anion transport | 372 | 22 |
| GO:BP | cellular lipid metabolic process | 994 | 38 |
| GO:BP | primary metabolic process | 10243 | 189 |
| GO:BP | peptide metabolic process | 835 | 34 |
| GO:BP | sulfur compound metabolic process | 317 | 20 |
| GO:BP | amide biosynthetic process | 793 | 32 |
| GO:BP | hormone metabolic process | 219 | 16 |
| GO:BP | cellular catabolic process | 2059 | 58 |
| GO:BP | cellular modified amino acid metabolic process | 179 | 14 |
| GO:BP | organic hydroxy compound metabolic process | 527 | 24 |
| GO:BP | nucleobase-containing small molecule metabolic process | 537 | 24 |
| GO:BP | fatty acid metabolic process | 425 | 21 |
| GO:BP | organic acid biosynthetic process | 290 | 17 |
| GO:BP | carboxylic acid transport | 297 | 17 |
| GO:BP | monocarboxylic acid transport | 121 | 11 |
| GO:BP | lipid catabolic process | 335 | 18 |
| GO:BP | alpha-amino acid biosynthetic process | 62 | 8 |
| GO:BP | carboxylic acid biosynthetic process | 282 | 16 |
| GO:BP | cellular amino acid biosynthetic process | 62 | 8 |
| GO:BP | biosynthetic process | 5882 | 118 |
| GO:BP | nitrogen compound metabolic process | 9669 | 173 |
| GO:BP | nucleotide metabolic process | 466 | 21 |
| GO:BP | nucleoside phosphate metabolic process | 476 | 21 |
| GO:BP | translation | 657 | 25 |
| GO:BP | monocarboxylic acid catabolic process | 122 | 10 |
| GO:BP | regulation of biological quality | 3876 | 84 |
| GO:BP | peptide biosynthetic process | 677 | 25 |
| GO:BP | L-serine biosynthetic process | 4 | 3 |
| GO:BP | alpha-amino acid catabolic process | 80 | 8 |
| GO:BP | organic substance biosynthetic process | 5779 | 113 |
| GO:BP | nucleotide biosynthetic process | 229 | 13 |
| GO:BP | nucleoside phosphate biosynthetic process | 232 | 13 |
| GO:BP | organonitrogen compound catabolic process | 1249 | 36 |
| GO:BP | steroid metabolic process | 306 | 15 |
| GO:BP | alcohol metabolic process | 344 | 16 |
| GO:BP | cellular amino acid catabolic process | 92 | 8 |
| GO:BP | cellular lipid catabolic process | 214 | 12 |
| GO:BP | organophosphate metabolic process | 891 | 28 |
| GO:BP | detoxification | 123 | 9 |
| GO:BP | NAD biosynthetic process | 16 | 4 |
| GO:BP | serine family amino acid biosynthetic process | 16 | 4 |
| GO:BP | cholesterol biosynthetic process | 50 | 6 |
| GO:BP | secondary alcohol biosynthetic process | 50 | 6 |
| GO:BP | fatty acid catabolic process | 99 | 8 |
| GO:BP | cellular biosynthetic process | 5715 | 109 |
| GO:BP | cytoplasmic translation | 101 | 8 |
| GO:BP | cellular hormone metabolic process | 135 | 9 |
| GO:BP | sulfur compound biosynthetic process | 106 | 8 |
| GO:BP | sterol biosynthetic process | 56 | 6 |
| GO:BP | pyridine nucleotide biosynthetic process | 20 | 4 |
| GO:BP | cellular nitrogen compound metabolic process | 6201 | 115 |
| GO:BP | serine family amino acid metabolic process | 37 | 5 |
| GO:BP | nicotinamide nucleotide biosynthetic process | 20 | 4 |
| GO:BP | acetyl-CoA metabolic process | 37 | 5 |
| GO:BP | L-serine metabolic process | 8 | 3 |
| GO:BP | secondary alcohol metabolic process | 141 | 9 |
| GO:BP | transmembrane transport | 1533 | 39 |
| GO:BP | purine-containing compound metabolic process | 406 | 16 |
| GO:BP | fatty acid oxidation | 114 | 8 |
| GO:BP | organophosphate biosynthetic process | 500 | 18 |
| GO:BP | lipid localization | 459 | 17 |
| GO:BP | amine metabolic process | 119 | 8 |
| GO:BP | pyridine-containing compound biosynthetic process | 23 | 4 |
| GO:BP | lipid oxidation | 120 | 8 |
| GO:BP | ion transport | 1572 | 39 |
| GO:BP | lipid biosynthetic process | 647 | 21 |
| GO:BP | aspartate family amino acid metabolic process | 43 | 5 |
| GO:BP | regulation of hormone levels | 559 | 19 |
| GO:BP | negative regulation of ubiquitin protein ligase activity | 11 | 3 |
| GO:BP | thyroid hormone transport | 11 | 3 |
| GO:BP | steroid biosynthetic process | 161 | 9 |
| GO:BP | glutathione metabolic process | 70 | 6 |
| GO:BP | vitamin metabolic process | 70 | 6 |
| GO:BP | cholesterol metabolic process | 129 | 8 |
| GO:BP | glutamine family amino acid metabolic process | 71 | 6 |
| GO:BP | negative regulation of ERBB signaling pathway | 27 | 4 |
| GO:BP | thyroid hormone metabolic process | 27 | 4 |
| GO:BP | carbohydrate derivative metabolic process | 975 | 27 |
| GO:BP | lipid transport | 401 | 15 |
| GO:BP | astral microtubule organization | 12 | 3 |
| GO:BP | response to toxic substance | 240 | 11 |
| GO:BP | response to zinc ion | 49 | 5 |
| GO:BP | carbohydrate metabolic process | 587 | 19 |
| GO:BP | L-alanine import across plasma membrane | 3 | 2 |
| GO:BP | alcohol biosynthetic process | 136 | 8 |
| GO:BP | nicotinamide nucleotide metabolic process | 29 | 4 |
| GO:BP | sterol metabolic process | 137 | 8 |
| GO:BP | pyridine nucleotide metabolic process | 29 | 4 |
| GO:BP | indolalkylamine metabolic process | 13 | 3 |
| GO:BP | tryptophan metabolic process | 13 | 3 |
| GO:BP | short-chain fatty acid metabolic process | 13 | 3 |
| GO:BP | water-soluble vitamin metabolic process | 30 | 4 |
| GO:BP | aromatic amino acid family metabolic process | 30 | 4 |
| GO:BP | ribonucleoside bisphosphate metabolic process | 110 | 7 |
| GO:BP | cellular amine metabolic process | 110 | 7 |
| GO:BP | purine nucleoside bisphosphate metabolic process | 110 | 7 |
| GO:BP | nucleoside bisphosphate metabolic process | 110 | 7 |
| GO:BP | lipid modification | 218 | 10 |
| GO:BP | purine nucleotide metabolic process | 385 | 14 |
| GO:BP | pyridine-containing compound metabolic process | 33 | 4 |
| GO:BP | response to copper ion | 33 | 4 |
| GO:BP | sulfur amino acid metabolic process | 33 | 4 |
| GO:BP | response to metal ion | 388 | 14 |
| GO:BP | L-alanine transmembrane transport | 4 | 2 |
| GO:BP | terpenoid metabolic process | 85 | 6 |
| GO:BP | N-glycan processing | 16 | 3 |
| GO:BP | gap junction assembly | 16 | 3 |
| GO:BP | glycine metabolic process | 16 | 3 |
| GO:BP | formation of cytoplasmic translation initiation complex | 16 | 3 |
| GO:BP | cytoplasmic translational initiation | 35 | 4 |
| GO:BP | response to iron ion | 36 | 4 |
| GO:BP | sodium-independent organic anion transport | 17 | 3 |
| GO:BP | primary alcohol metabolic process | 90 | 6 |
| GO:BP | glycerolipid catabolic process | 62 | 5 |
| GO:CC | cytoplasm | 11093 | 219 |
| GO:CC | cytosolic ribosome | 112 | 14 |
| GO:CC | cytosol | 3849 | 95 |
| GO:CC | cytosolic small ribosomal subunit | 45 | 9 |
| GO:CC | intracellular anatomical structure | 14111 | 234 |
| GO:CC | ribosomal subunit | 200 | 15 |
| GO:CC | small ribosomal subunit | 79 | 10 |
| GO:CC | brush border | 134 | 12 |
| GO:CC | ribosome | 236 | 15 |
| GO:CC | cluster of actin-based cell projections | 193 | 13 |
| GO:CC | brush border membrane | 73 | 8 |
| GO:CC | intracellular organelle | 12510 | 205 |
| GO:CC | organelle | 12827 | 208 |
| GO:CC | intracellular membrane-bounded organelle | 11363 | 189 |
| GO:CC | membrane-bounded organelle | 11812 | 194 |
| GO:CC | endomembrane system | 4006 | 83 |
| GO:CC | cellular anatomical entity | 19567 | 280 |
| GO:CC | endoplasmic reticulum | 1761 | 44 |
| GO:CC | mitochondrion | 1827 | 45 |
| GO:CC | organelle envelope | 1176 | 32 |
| GO:CC | envelope | 1176 | 32 |
| GO:CC | ribonucleoprotein complex | 725 | 23 |
| GO:CC | eukaryotic translation initiation factor 3 complex, eIF3e | 2 | 2 |
| GO:CC | organelle membrane | 3076 | 64 |
| GO:CC | eukaryotic translation elongation factor 1 complex | 3 | 2 |
| GO:CC | basal part of cell | 291 | 12 |
| GO:CC | mitochondrial matrix | 341 | 13 |
| GO:CC | basal plasma membrane | 272 | 11 |
| GO:CC | nuclear envelope | 460 | 15 |
| GO:CC | cytosolic large ribosomal subunit | 64 | 5 |
| GO:CC | vacuole | 562 | 17 |
| GO:CC | lytic vacuole | 468 | 15 |
| GO:CC | lysosome | 468 | 15 |
| GO:CC | apical part of cell | 474 | 15 |
| GO:CC | apical plasma membrane | 388 | 13 |
| GO:CC | polysome | 70 | 5 |
| GO:CC | cell junction | 2071 | 43 |
| GO:CC | collagen network | 7 | 2 |
| GO:CC | network-forming collagen trimer | 7 | 2 |
| GO:CC | collagen type IV trimer | 7 | 2 |
| GO:CC | basement membrane collagen trimer | 7 | 2 |
| GO:MF | catalytic activity | 5665 | 135 |
| GO:MF | oxidoreductase activity | 815 | 35 |
| GO:MF | structural constituent of ribosome | 172 | 14 |
| GO:MF | rRNA binding | 69 | 9 |
| GO:MF | 5S rRNA binding | 13 | 5 |
| GO:MF | identical protein binding | 2140 | 57 |
| GO:MF | transporter activity | 1137 | 37 |
| GO:MF | organic acid transmembrane transporter activity | 156 | 12 |
| GO:MF | carboxylic acid transmembrane transporter activity | 155 | 12 |
| GO:MF | flavin adenine dinucleotide binding | 90 | 9 |
| GO:MF | secondary active transmembrane transporter activity | 232 | 14 |
| GO:MF | transmembrane transporter activity | 1053 | 34 |
| GO:MF | monocarboxylic acid transmembrane transporter activity | 56 | 7 |
| GO:MF | anion transmembrane transporter activity | 295 | 15 |
| GO:MF | lyase activity | 198 | 12 |
| GO:MF | dipeptidase activity | 15 | 4 |
| GO:MF | amide binding | 367 | 16 |
| GO:MF | active transmembrane transporter activity | 346 | 15 |
| GO:MF | carbon-carbon lyase activity | 55 | 6 |
| GO:MF | metallodipeptidase activity | 8 | 3 |
| GO:MF | organic anion transmembrane transporter activity | 172 | 10 |
| GO:MF | RNA binding | 1267 | 34 |
| GO:MF | asparaginase activity | 2 | 2 |
| GO:MF | ubiquitin ligase inhibitor activity | 9 | 3 |
| GO:MF | ubiquitin-protein transferase inhibitor activity | 10 | 3 |
| GO:MF | transferase activity, transferring alkyl or aryl (other than methyl) groups | 65 | 6 |
| GO:MF | single-stranded RNA binding | 92 | 7 |
| GO:MF | structural molecule activity | 612 | 20 |
| GO:MF | mRNA 5’-UTR binding | 25 | 4 |
| GO:MF | acyl-CoA dehydrogenase activity | 11 | 3 |
| GO:MF | small molecule binding | 2543 | 55 |
| GO:MF | oleic acid binding | 3 | 2 |
| GO:MF | D5 dopamine receptor binding | 3 | 2 |
| GO:MF | carbon-nitrogen lyase activity | 13 | 3 |
| GO:MF | hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides | 77 | 6 |
| GO:MF | symporter activity | 140 | 8 |
| GO:MF | vitamin binding | 141 | 8 |
| GO:MF | inorganic anion transmembrane transporter activity | 142 | 8 |
| GO:MF | NADP binding | 55 | 5 |
| GO:MF | translation regulator activity | 145 | 8 |
| GO:MF | translation regulator activity, nucleic acid binding | 113 | 7 |
| GO:MF | glutathione disulfide oxidoreductase activity | 4 | 2 |
| GO:MF | hormone binding | 85 | 6 |
| GO:MF | sodium-independent organic anion transmembrane transporter activity | 16 | 3 |
| GO:MF | binding | 14895 | 229 |
| GO:MF | carboxylic ester hydrolase activity | 153 | 8 |
| GO:MF | hydrolase activity, acting on ester bonds | 735 | 21 |
| GO:MF | oxidoreductase activity, acting on the CH-CH group of donors | 60 | 5 |
| GO:MF | carboxy-lyase activity | 36 | 4 |
| GO:MF | intramolecular oxidoreductase activity, transposing C=C bonds | 17 | 3 |
| GO:MF | lipase activity | 124 | 7 |
| GO:MF | protein binding | 10189 | 166 |
| GO:MF | AMP binding | 18 | 3 |
| GO:MF | long-chain-acyl-CoA dehydrogenase activity | 5 | 2 |
| GO:MF | aminoacylase activity | 5 | 2 |
| GO:MF | exopeptidase activity | 96 | 6 |
| GO:MF | translation factor activity, RNA binding | 96 | 6 |
| GO:MF | RNA polymerase II general transcription initiation factor binding | 19 | 3 |
| GO:MF | carboxypeptidase activity | 41 | 4 |
| GO:MF | sialyltransferase activity | 20 | 3 |
| GO:MF | peptide binding | 290 | 11 |
| GO:MF | lysophospholipase activity | 20 | 3 |
| GO:MF | acetyl-CoA C-acetyltransferase activity | 6 | 2 |
| GO:MF | steroid delta-isomerase activity | 6 | 2 |
| GO:MF | alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity | 6 | 2 |
| GO:MF | ubiquitin-protein transferase regulator activity | 22 | 3 |
| GO:MF | general transcription initiation factor binding | 45 | 4 |
| GO:MF | mRNA binding | 394 | 13 |
| HP | Abnormal radial artery morphology | 18 | 5 |
| HP | Elevated red cell adenosine deaminase level | 18 | 5 |
| HP | Radial artery aplasia | 18 | 5 |
| HP | Macrocytic dyserythropoietic anemia | 19 | 5 |
| HP | Macrocytic anemia | 58 | 8 |
| HP | Thrombocytosis | 46 | 7 |
| HP | Abnormal circulating serine concentration | 5 | 3 |
| HP | Increased mean corpuscular volume | 35 | 6 |
| HP | Malignant genitourinary tract tumor | 22 | 5 |
| HP | Adenocarcinoma of the colon | 23 | 5 |
| HP | Erythroid hypoplasia | 21 | 5 |
| HP | Pure red cell aplasia | 23 | 5 |
| HP | Nonimmune hydrops fetalis | 38 | 6 |
| HP | Abnormal enzyme/coenzyme activity | 477 | 22 |
| HP | Persistence of hemoglobin F | 25 | 5 |
| HP | Adenocarcinoma of the large intestine | 26 | 5 |
| HP | Abnormality of the thenar eminence | 25 | 5 |
| HP | Osteomalacia | 26 | 5 |
| HP | Abnormal erythrocyte enzyme level | 26 | 5 |
| HP | Osteosarcoma | 28 | 5 |
| HP | Normochromic anemia | 29 | 5 |
| HP | Reticulocytopenia | 29 | 5 |
| HP | Abnormal mean corpuscular volume | 45 | 6 |
| HP | Increased lactate dehydrogenase level | 31 | 5 |
| HP | Adenocarcinoma of the intestines | 31 | 5 |
| HP | Hypoglycinemia | 2 | 2 |
| HP | Duplication of thumb phalanx | 49 | 6 |
| HP | Elevated 8(9)-cholestenol | 2 | 2 |
| HP | Elevated 8-dehydrocholesterol | 2 | 2 |
| HP | Partial duplication of thumb phalanx | 33 | 5 |
| HP | Abnormal number of erythroid precursors | 34 | 5 |
| HP | Abnormal platelet count | 351 | 17 |
| HP | Systemic lupus erythematosus | 34 | 5 |
| HP | Neoplasm of the gastrointestinal tract | 261 | 14 |
| HP | Partial duplication of the phalanx of hand | 35 | 5 |
| HP | Rickets | 36 | 5 |
| KEGG | Metabolic pathways | 1563 | 66 |
| KEGG | Ribosome | 169 | 14 |
| KEGG | Coronavirus disease - COVID-19 | 241 | 16 |
| KEGG | Steroid biosynthesis | 20 | 5 |
| KEGG | Glutathione metabolism | 71 | 8 |
| KEGG | Glycine, serine and threonine metabolism | 39 | 6 |
| KEGG | Glyoxylate and dicarboxylate metabolism | 31 | 5 |
| REAC | GTP hydrolysis and joining of the 60S ribosomal subunit | 109 | 18 |
| REAC | L13a-mediated translational silencing of Ceruloplasmin expression | 108 | 18 |
| REAC | Eukaryotic Translation Initiation | 116 | 18 |
| REAC | Cap-dependent Translation Initiation | 116 | 18 |
| REAC | Translation initiation complex formation | 56 | 13 |
| REAC | Ribosomal scanning and start codon recognition | 56 | 13 |
| REAC | Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S | 57 | 13 |
| REAC | Formation of a pool of free 40S subunits | 98 | 16 |
| REAC | Formation of the ternary complex, and subsequently, the 43S complex | 49 | 12 |
| REAC | Metabolism | 1679 | 70 |
| REAC | SRP-dependent cotranslational protein targeting to membrane | 89 | 14 |
| REAC | Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) | 91 | 14 |
| REAC | Translation | 217 | 20 |
| REAC | Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) | 110 | 14 |
| REAC | Nonsense-Mediated Decay (NMD) | 110 | 14 |
| REAC | Metabolism of amino acids and derivatives | 234 | 18 |
| REAC | Major pathway of rRNA processing in the nucleolus and cytosol | 167 | 15 |
| REAC | rRNA processing in the nucleus and cytosol | 167 | 15 |
| REAC | rRNA processing | 167 | 15 |
| REAC | Sialic acid metabolism | 30 | 6 |
| REAC | SLC-mediated transmembrane transport | 218 | 15 |
| REAC | Synthesis of substrates in N-glycan biosythesis | 58 | 7 |
| REAC | Biosynthesis of the N-glycan precursor (dolichol lipid-linked oligosaccharide, LLO) and transfer to a nascent protein | 68 | 7 |
| REAC | Biological oxidations | 204 | 12 |
| REAC | ARL13B-mediated ciliary trafficking of INPP5E | 3 | 2 |
| REAC | Cholesterol biosynthesis | 25 | 4 |
| REAC | Metabolism of nucleotides | 91 | 7 |
| REAC | Cholesterol biosynthesis via desmosterol | 4 | 2 |
| REAC | Cholesterol biosynthesis via lathosterol | 4 | 2 |
| REAC | Metabolism of RNA | 532 | 21 |
| TF | Factor: E2F-1; motif: GNGGGCGGGRMN | 14228 | 235 |
| TF | Factor: BEN; motif: CAGCGRNV | 16234 | 256 |
| TF | Factor: FOXN4; motif: NNWANNCGWMCGCGTCNNNNMT | 16009 | 253 |
| TF | Factor: Hes1; motif: NNCACGYGNN | 15504 | 244 |
| TF | Factor: Mxi1; motif: NCACGTGGSNGNNNN | 3073 | 69 |
| TF | Factor: USF2; motif: NNNCCACGTGACN | 3892 | 82 |
| TF | Factor: Hes1; motif: NNCACGYGNN; match class: 1 | 11386 | 191 |
| TF | Factor: ZF5; motif: GSGCGCGR | 14821 | 234 |
| TF | Factor: GKLF; motif: NNNRGGNGNGGSN | 15302 | 240 |
| TF | Factor: Zfp536; motif: NCGGAKG | 6308 | 118 |
| TF | Factor: BCL6B; motif: NNNNCCGCCCCWNNNN | 13664 | 219 |
| TF | Factor: ZF5; motif: NRNGNGCGCGCWN | 14469 | 228 |
| TF | Factor: E2F-3; motif: GGCGGGN | 11268 | 186 |
| TF | Factor: Kaiso; motif: SARNYCTCGCGAGAN | 13491 | 215 |
| TF | Factor: Klf17; motif: NGGGCGG | 6533 | 119 |
| TF | Factor: FOXN4; motif: NNWANNCGWMCGCGTCNNNNMT; match class: 1 | 12768 | 205 |
| TF | Factor: USF1; motif: NNNNGTCACGTGGN | 3312 | 69 |
| TF | Factor: GLI; motif: NSTGGGTGGTCY | 9871 | 166 |
| TF | Factor: BEN; motif: CAGCGRNV; match class: 1 | 11980 | 194 |
| TF | Factor: E2F-1; motif: NTTSGCGG | 6957 | 124 |
| TF | Factor: AR; motif: GNNCNNNNTGTTCTN; match class: 1 | 565 | 19 |
| TF | Factor: c-Myc; motif: KACCACGTGSYY | 5491 | 102 |
| TF | Factor: N-Myc; motif: NNCCACGTGNNN | 4316 | 84 |
| TF | Factor: Egr-1; motif: WTGCGTGGGCGK | 4340 | 84 |
| WP | Cytoplasmic Ribosomal Proteins | 81 | 12 |
| WP | Cholesterol metabolism (includes both Bloch and Kandutsch-Russell pathways) | 51 | 6 |
| WP | mRNA processing | 444 | 22 |
| WP | Translation Factors | 49 | 6 |
| WP | One carbon metabolism and related pathways | 52 | 6 |
| WP | Amino Acid metabolism | 95 | 8 |
2.2.8 Functional Enrichment - Kidney TCDD-AhR Regulated
kable(Kidney_Interx_PathwayEnrichment$result %>% dplyr::select(source, term_name, term_size, intersection_size),
table.attr = "class=\"striped\"", format = "html")| source | term_name | term_size | intersection_size |
|---|---|---|---|
| GO:BP | response to decreased oxygen levels | 341 | 4 |
| GO:BP | tube development | 1137 | 6 |
| GO:BP | response to organic substance | 3418 | 9 |
| GO:BP | response to organic cyclic compound | 1043 | 6 |
| GO:BP | response to hypoxia | 326 | 4 |
| GO:BP | response to oxygen levels | 368 | 4 |
| GO:BP | cellular response to oxygen levels | 175 | 3 |
| GO:BP | regulation of B cell differentiation | 30 | 2 |
| GO:BP | estrogen metabolic process | 27 | 2 |
| GO:BP | enzyme linked receptor protein signaling pathway | 916 | 5 |
| GO:BP | cellular response to hypoxia | 146 | 3 |
| GO:BP | fatty acid metabolic process | 425 | 4 |
| GO:BP | tube morphogenesis | 911 | 5 |
| GO:BP | cellular response to decreased oxygen levels | 156 | 3 |
| GO:BP | positive regulation of catabolic process | 481 | 4 |
| GO:BP | reproductive structure development | 503 | 4 |
| GO:BP | reproductive system development | 508 | 4 |
| GO:BP | catabolic process | 2399 | 7 |
| GO:BP | cellular response to organic substance | 2453 | 7 |
| GO:BP | lipid modification | 218 | 3 |
| GO:BP | transmembrane receptor protein tyrosine kinase signaling pathway | 587 | 4 |
| GO:BP | negative regulation of canonical Wnt signaling pathway involved in controlling type B pancreatic cell proliferation | 1 | 1 |
| GO:BP | response to abiotic stimulus | 1177 | 5 |
| GO:BP | tissue development | 1923 | 6 |
| GO:BP | phytanic acid metabolic process | 1 | 1 |
| GO:BP | response to raffinose | 1 | 1 |
| GO:BP | epidermal growth factor receptor signaling pathway via MAPK cascade | 1 | 1 |
| GO:BP | GDP-L-fucose salvage | 1 | 1 |
| GO:BP | convergent extension involved in somitogenesis | 1 | 1 |
| GO:BP | dibenzo-p-dioxin catabolic process | 1 | 1 |
| GO:BP | circulatory system development | 1174 | 5 |
| GO:BP | monocarboxylic acid metabolic process | 616 | 4 |
| GO:BP | cellular response to organic cyclic compound | 595 | 4 |
| GO:BP | blood vessel morphogenesis | 647 | 4 |
| GO:BP | platelet-derived growth factor receptor signaling pathway | 60 | 2 |
| GO:BP | cellular response to raffinose | 1 | 1 |
| GO:BP | regulation of cell cycle process | 599 | 4 |
| GO:BP | stromal-epithelial cell signaling involved in prostate gland development | 1 | 1 |
| GO:BP | organic substance catabolic process | 1985 | 6 |
| GO:BP | positive regulation of fat cell differentiation | 67 | 2 |
| GO:BP | regulation of morphogenesis of an epithelium | 69 | 2 |
| GO:BP | cellular catabolic process | 2059 | 6 |
| GO:BP | blood vessel development | 743 | 4 |
| GO:BP | lipid metabolic process | 1344 | 5 |
| GO:BP | cellular response to chemical stimulus | 3097 | 7 |
| GO:BP | ERK1 and ERK2 cascade | 344 | 3 |
| GO:BP | vasculature development | 773 | 4 |
| GO:BP | MAPK cascade | 771 | 4 |
| GO:BP | head development | 805 | 4 |
| GO:BP | regulation of epithelial cell proliferation | 359 | 3 |
| GO:BP | insecticide metabolic process | 2 | 1 |
| GO:BP | small molecule catabolic process | 346 | 3 |
| GO:BP | regulation of planar cell polarity pathway involved in axis elongation | 2 | 1 |
| GO:BP | negative regulation of planar cell polarity pathway involved in axis elongation | 2 | 1 |
| GO:BP | Wnt signaling pathway involved in dorsal/ventral axis specification | 2 | 1 |
| GO:BP | regulation of Wnt signaling pathway involved in dorsal/ventral axis specification | 2 | 1 |
| GO:BP | negative regulation of Wnt signaling pathway involved in dorsal/ventral axis specification | 2 | 1 |
| GO:BP | canonical Wnt signaling pathway involved in regulation of type B pancreatic cell proliferation | 2 | 1 |
| GO:BP | regulation of canonical Wnt signaling pathway involved in controlling type B pancreatic cell proliferation | 2 | 1 |
| GO:BP | septum transversum development | 2 | 1 |
| GO:BP | proepicardium development | 2 | 1 |
| GO:BP | oxoacid metabolic process | 908 | 4 |
| GO:BP | vasculogenesis | 90 | 2 |
| GO:BP | carboxylic acid metabolic process | 896 | 4 |
| GO:BP | response to fibroblast growth factor | 104 | 2 |
| GO:BP | cellular response to interleukin-1 | 103 | 2 |
| GO:BP | cellular response to fibroblast growth factor stimulus | 97 | 2 |
| GO:BP | response to vitamin | 103 | 2 |
| GO:BP | negative regulation of myeloid cell differentiation | 97 | 2 |
| GO:BP | regulation of cell cycle | 898 | 4 |
| GO:BP | response to chemical | 5544 | 9 |
| GO:BP | regulation of fibroblast proliferation | 102 | 2 |
| GO:BP | fibroblast proliferation | 104 | 2 |
| GO:BP | positive regulation of cellular catabolic process | 414 | 3 |
| GO:BP | GDP-L-fucose biosynthetic process | 3 | 1 |
| GO:BP | negative regulation of B cell differentiation | 3 | 1 |
| GO:BP | regulation of catabolic process | 893 | 4 |
| GO:BP | positive regulation of aggrephagy | 3 | 1 |
| GO:BP | Wnt signaling pathway involved in somitogenesis | 3 | 1 |
| GO:BP | positive regulation of intracellular mRNA localization | 3 | 1 |
| GO:BP | methyl-branched fatty acid metabolic process | 3 | 1 |
| GO:BP | neural crest cell fate commitment | 3 | 1 |
| GO:BP | fatty acid catabolic process | 99 | 2 |
| GO:BP | lipid hydroxylation | 3 | 1 |
| GO:BP | regulation of intracellular mRNA localization | 3 | 1 |
| GO:BP | positive regulation of signal transduction | 1506 | 5 |
| GO:BP | regulation of aggrephagy | 3 | 1 |
| GO:BP | positive regulation of canonical Wnt signaling pathway | 106 | 2 |
| GO:BP | epithelial cell proliferation | 424 | 3 |
| GO:BP | regulation of mitotic cell cycle | 425 | 3 |
| GO:BP | organic acid metabolic process | 944 | 4 |
| GO:BP | fatty acid oxidation | 114 | 2 |
| GO:BP | response to 2,3,7,8-tetrachlorodibenzodioxine | 4 | 1 |
| GO:BP | lipid oxidation | 120 | 2 |
| GO:BP | monocarboxylic acid catabolic process | 122 | 2 |
| GO:BP | cellular lipid metabolic process | 994 | 4 |
| GO:BP | cellular response to heparin | 4 | 1 |
| GO:BP | dibenzo-p-dioxin metabolic process | 4 | 1 |
| GO:BP | axis elongation involved in somitogenesis | 4 | 1 |
| GO:BP | GDP-L-fucose metabolic process | 4 | 1 |
| GO:BP | female gonad development | 123 | 2 |
| GO:BP | development of primary female sexual characteristics | 128 | 2 |
| GO:BP | regulation of midbrain dopaminergic neuron differentiation | 5 | 1 |
| GO:BP | regulation of myeloid leukocyte differentiation | 125 | 2 |
| GO:BP | small molecule metabolic process | 1713 | 5 |
| GO:BP | animal organ development | 3617 | 7 |
| GO:BP | canonical Wnt signaling pathway involved in regulation of cell proliferation | 5 | 1 |
| GO:BP | stem cell fate commitment | 5 | 1 |
| GO:BP | planar cell polarity pathway involved in axis elongation | 5 | 1 |
| GO:BP | response to nematode | 5 | 1 |
| GO:BP | reproduction | 1775 | 5 |
| GO:BP | response to interleukin-1 | 131 | 2 |
| GO:BP | phosphatidylinositol 3-kinase signaling | 127 | 2 |
| GO:BP | reproductive process | 1774 | 5 |
| GO:BP | response to heparin | 5 | 1 |
| GO:BP | positive regulation of Wnt signaling pathway | 136 | 2 |
| GO:BP | positive regulation of cell communication | 1725 | 5 |
| GO:BP | positive regulation of hyaluronan biosynthetic process | 5 | 1 |
| GO:BP | nuclear-transcribed mRNA catabolic process, deadenylation-independent decay | 5 | 1 |
| GO:BP | fatty acid beta-oxidation using acyl-CoA oxidase | 5 | 1 |
| GO:BP | positive regulation of signaling | 1732 | 5 |
| GO:BP | cellular hormone metabolic process | 135 | 2 |
| GO:BP | digestive tract development | 137 | 2 |
| GO:BP | female sex differentiation | 143 | 2 |
| GO:BP | cell cycle process | 1082 | 4 |
| GO:BP | gland development | 513 | 3 |
| GO:BP | regulation of fat cell differentiation | 142 | 2 |
| GO:BP | system development | 4876 | 8 |
| GO:BP | anatomical structure morphogenesis | 2715 | 6 |
| GO:BP | prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis | 6 | 1 |
| GO:BP | negative regulation of non-canonical Wnt signaling pathway | 6 | 1 |
| GO:BP | coumarin metabolic process | 6 | 1 |
| GO:BP | B cell differentiation | 147 | 2 |
| GO:BP | phenylpropanoid metabolic process | 6 | 1 |
| GO:BP | response to iron(III) ion | 6 | 1 |
| GO:BP | regulation of branching involved in prostate gland morphogenesis | 6 | 1 |
| GO:BP | prostate glandular acinus morphogenesis | 6 | 1 |
| GO:BP | epithelial tube formation | 151 | 2 |
| GO:BP | digestive system development | 152 | 2 |
| GO:BP | positive regulation of biological process | 6305 | 9 |
| GO:BP | obsolete oxidation-reduction process | 548 | 3 |
| GO:BP | fatty acid alpha-oxidation | 7 | 1 |
| GO:BP | 9-cis-retinoic acid metabolic process | 7 | 1 |
| GO:BP | phosphatidylinositol-mediated signaling | 162 | 2 |
| GO:BP | regulation of biological quality | 3876 | 7 |
| GO:BP | keratinocyte apoptotic process | 7 | 1 |
| GO:BP | regulation of keratinocyte apoptotic process | 7 | 1 |
| GO:BP | regulation of hormone levels | 559 | 3 |
| GO:BP | 9-cis-retinoic acid biosynthetic process | 7 | 1 |
| GO:BP | tube formation | 163 | 2 |
| GO:BP | epithelium development | 1171 | 4 |
| GO:BP | inositol lipid-mediated signaling | 165 | 2 |
| GO:BP | placenta development | 172 | 2 |
| GO:BP | positive regulation of neurotrophin TRK receptor signaling pathway | 8 | 1 |
| GO:BP | regulation of dopaminergic neuron differentiation | 8 | 1 |
| GO:BP | aggrephagy | 8 | 1 |
| GO:BP | regulation of epithelial tube formation | 8 | 1 |
| GO:BP | positive regulation of epithelial tube formation | 8 | 1 |
| GO:BP | chorio-allantoic fusion | 8 | 1 |
| GO:BP | response to herbicide | 8 | 1 |
| GO:BP | developmental process involved in reproduction | 1191 | 4 |
| GO:BP | convergent extension involved in axis elongation | 8 | 1 |
| GO:BP | regulation of lymphocyte differentiation | 178 | 2 |
| GO:BP | positive regulation of protein localization to early endosome | 9 | 1 |
| GO:BP | regulation of hyaluronan biosynthetic process | 9 | 1 |
| GO:BP | regulation of protein localization to early endosome | 9 | 1 |
| GO:BP | positive regulation of peroxisome proliferator activated receptor signaling pathway | 9 | 1 |
| GO:BP | neural tube development | 181 | 2 |
| GO:BP | positive regulation of fibroblast apoptotic process | 9 | 1 |
| GO:BP | maternal process involved in parturition | 9 | 1 |
| GO:BP | response to nutrient | 187 | 2 |
| GO:BP | cell population proliferation | 2072 | 5 |
| GO:BP | negative regulation of fibroblast apoptotic process | 10 | 1 |
| GO:BP | convergent extension involved in gastrulation | 10 | 1 |
| GO:BP | monocarboxylic acid biosynthetic process | 194 | 2 |
| GO:BP | positive regulation of execution phase of apoptosis | 10 | 1 |
| GO:BP | positive regulation of monocyte differentiation | 10 | 1 |
| GO:BP | positive regulation of cerebellar granule cell precursor proliferation | 11 | 1 |
| GO:BP | protein mono-ADP-ribosylation | 11 | 1 |
| GO:BP | mesendoderm development | 11 | 1 |
| GO:BP | negative regulation of erythrocyte differentiation | 11 | 1 |
| GO:BP | diterpenoid biosynthetic process | 11 | 1 |
| GO:BP | neural crest formation | 11 | 1 |
| GO:BP | cellular response to tumor necrosis factor | 198 | 2 |
| GO:BP | cellular response to steroid hormone stimulus | 205 | 2 |
| GO:BP | protein localization to early endosome | 11 | 1 |
| GO:BP | morphogenesis of a branching epithelium | 203 | 2 |
| GO:BP | positive regulation of epithelial cell proliferation | 205 | 2 |
| GO:BP | prostate glandular acinus development | 11 | 1 |
| GO:BP | response to stimulus | 9950 | 11 |
| GO:BP | bone trabecula formation | 11 | 1 |
| GO:BP | dorsal/ventral axis specification | 11 | 1 |
| GO:BP | retinoic acid biosynthetic process | 11 | 1 |
| GO:BP | multicellular organism development | 5441 | 8 |
| GO:BP | cellular lipid catabolic process | 214 | 2 |
| GO:BP | regulation of protein localization to endosome | 14 | 1 |
| GO:BP | flavonoid metabolic process | 14 | 1 |
| GO:BP | organic acid catabolic process | 228 | 2 |
| GO:BP | morphogenesis of a branching structure | 220 | 2 |
| GO:BP | myeloid leukocyte differentiation | 219 | 2 |
| GO:BP | regulation of myeloid cell differentiation | 217 | 2 |
| GO:BP | activation of cysteine-type endopeptidase activity | 14 | 1 |
| GO:BP | positive regulation of extrinsic apoptotic signaling pathway via death domain receptors | 13 | 1 |
| GO:BP | establishment or maintenance of transmembrane electrochemical gradient | 12 | 1 |
| GO:BP | mitotic cell cycle process | 666 | 3 |
| GO:BP | planar cell polarity pathway involved in neural tube closure | 12 | 1 |
| GO:BP | negative regulation of platelet-derived growth factor receptor signaling pathway | 13 | 1 |
| GO:BP | midbrain dopaminergic neuron differentiation | 14 | 1 |
| GO:BP | regulation of establishment of planar polarity involved in neural tube closure | 13 | 1 |
| GO:BP | hormone metabolic process | 219 | 2 |
| GO:BP | positive regulation of cell cycle process | 224 | 2 |
| GO:BP | positive regulation of response to stimulus | 2198 | 5 |
| GO:BP | nucleotide salvage | 14 | 1 |
| GO:BP | sodium ion export across plasma membrane | 14 | 1 |
| GO:BP | negative regulation of secretion | 207 | 2 |
| GO:BP | stress-activated MAPK cascade | 231 | 2 |
| GO:BP | regulation of MAPK cascade | 708 | 3 |
| GO:BP | protein kinase B signaling | 214 | 2 |
| GO:BP | branching involved in prostate gland morphogenesis | 13 | 1 |
| GO:BP | carboxylic acid catabolic process | 221 | 2 |
| GO:BP | response to tumor necrosis factor | 223 | 2 |
| GO:BP | regulation of Wnt signaling pathway, planar cell polarity pathway | 14 | 1 |
| GO:BP | bone trabecula morphogenesis | 14 | 1 |
| GO:BP | establishment of planar polarity involved in neural tube closure | 14 | 1 |
| GO:BP | protein auto-ADP-ribosylation | 12 | 1 |
| GO:BP | positive regulation of protein localization to endosome | 13 | 1 |
| GO:BP | regulation of type B pancreatic cell proliferation | 14 | 1 |
| GO:BP | parturition | 14 | 1 |
| GO:BP | response to insecticide | 13 | 1 |
| GO:BP | regulation of cerebellar granule cell precursor proliferation | 14 | 1 |
| GO:BP | cellular response to transforming growth factor beta stimulus | 231 | 2 |
| GO:BP | positive regulation of ERK1 and ERK2 cascade | 225 | 2 |
| GO:BP | cellular response to X-ray | 12 | 1 |
| GO:BP | cellular response to salt stress | 14 | 1 |
| GO:BP | cellular potassium ion homeostasis | 13 | 1 |
| GO:BP | cellular response to growth factor stimulus | 669 | 3 |
| GO:BP | hyaluronan biosynthetic process | 14 | 1 |
| GO:BP | positive regulation of epidermal growth factor-activated receptor activity | 13 | 1 |
| GO:BP | positive regulation of non-canonical Wnt signaling pathway | 14 | 1 |
| GO:BP | response to growth factor | 697 | 3 |
| GO:BP | positive regulation of protein catabolic process | 225 | 2 |
| GO:BP | intracellular mRNA localization | 12 | 1 |
| GO:BP | positive regulation of developmental process | 1412 | 4 |
| GO:BP | response to transforming growth factor beta | 235 | 2 |
| GO:BP | skeletal system morphogenesis | 237 | 2 |
| GO:BP | cellular response to prostaglandin E stimulus | 15 | 1 |
| GO:BP | negative regulation of JUN kinase activity | 15 | 1 |
| GO:BP | xenobiotic catabolic process | 15 | 1 |
| GO:BP | nucleotide-sugar biosynthetic process | 16 | 1 |
| GO:BP | cellular metabolic process | 10350 | 11 |
| GO:BP | establishment of planar polarity of embryonic epithelium | 16 | 1 |
| GO:BP | developmental growth | 739 | 3 |
| GO:BP | regulation of B cell activation | 248 | 2 |
| GO:BP | regulation of neurotrophin TRK receptor signaling pathway | 16 | 1 |
| GO:BP | regulation of multicellular organismal development | 1444 | 4 |
| GO:BP | convergent extension | 16 | 1 |
| GO:BP | negative regulation of osteoblast proliferation | 16 | 1 |
| GO:BP | regulation of canonical Wnt signaling pathway | 241 | 2 |
| GO:BP | 3’-UTR-mediated mRNA destabilization | 16 | 1 |
| GO:BP | regulation of cellular catabolic process | 745 | 3 |
| GO:BP | stress-activated protein kinase signaling cascade | 246 | 2 |
| GO:BP | intracellular receptor signaling pathway | 244 | 2 |
| GO:BP | positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay | 16 | 1 |
| GO:BP | regulation of peroxisome proliferator activated receptor signaling pathway | 16 | 1 |
| GO:BP | fat cell differentiation | 247 | 2 |
| GO:MF | hydroperoxy icosatetraenoate dehydratase activity | 7 | 2 |
| GO:MF | fucokinase activity | 1 | 1 |
| GO:MF | hydro-lyase activity | 61 | 2 |
| GO:MF | flavonoid 3’-monooxygenase activity | 1 | 1 |
| GO:MF | lyase activity | 198 | 3 |
| GO:MF | pristanoyl-CoA oxidase activity | 1 | 1 |
| GO:MF | prostaglandin-I synthase activity | 1 | 1 |
| GO:MF | carbon-oxygen lyase activity | 78 | 2 |
| GO:MF | vitamin D 24-hydroxylase activity | 2 | 1 |
| GO:MF | P-type potassium:proton transporter activity | 3 | 1 |
| GO:MF | estrogen 2-hydroxylase activity | 3 | 1 |
| GO:MF | ion binding | 5862 | 9 |
| GO:MF | oxidoreductase activity, acting on the CH-CH group of donors, oxygen as acceptor | 9 | 1 |
| GO:MF | oxidoreductase activity, acting on diphenols and related substances as donors | 7 | 1 |
| GO:MF | heme binding | 183 | 2 |
| GO:MF | thiamine pyrophosphate binding | 8 | 1 |
| GO:MF | tetrapyrrole binding | 192 | 2 |
| GO:MF | metal ion binding | 4043 | 7 |
| GO:MF | P-type sodium transporter activity | 9 | 1 |
| GO:MF | P-type sodium:potassium-exchanging transporter activity | 9 | 1 |
| GO:MF | acyl-CoA oxidase activity | 6 | 1 |
| GO:MF | monooxygenase activity | 159 | 2 |
| GO:MF | P-type potassium transmembrane transporter activity | 11 | 1 |
| GO:MF | cation binding | 4138 | 7 |
| GO:MF | iron ion binding | 211 | 2 |
| GO:MF | estrogen 16-alpha-hydroxylase activity | 12 | 1 |
| GO:MF | oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen | 217 | 2 |
| GO:MF | P-type proton-exporting transporter activity | 15 | 1 |
| GO:MF | protein ADP-ribosylase activity | 15 | 1 |
| GO:MF | heterocyclic compound binding | 5672 | 8 |
| GO:MF | sulfur compound binding | 256 | 2 |
| GO:MF | organic cyclic compound binding | 5768 | 8 |
| REAC | Fatty acid metabolism | 169 | 4 |
| REAC | Peroxisomal lipid metabolism | 27 | 2 |
| REAC | Sterols are 12-hydroxylated by CYP8B1 | 1 | 1 |
| REAC | Cytochrome P450 - arranged by substrate type | 71 | 2 |
| REAC | Peroxisomal protein import | 61 | 2 |
| REAC | Metabolism of lipids | 573 | 4 |
| REAC | Arachidonic acid metabolism | 61 | 2 |
| REAC | Biosynthesis of protectins | 3 | 1 |
| WP | Eicosanoid metabolism via Cyclo Oxygenases (COX) | 31 | 2 |
2.2.9 Functional Enrichment - Liver and Kidney Ahr Regulated
kable(TissueIntersect_Ahr_PathwayEnrichment$result %>% dplyr::select(source, term_name, term_size, intersection_size),
table.attr = "class=\"striped\"", format = "html")| source | term_name | term_size | intersection_size |
|---|---|---|---|
| GO:BP | oxoacid metabolic process | 908 | 11 |
| GO:BP | carboxylic acid metabolic process | 896 | 11 |
| GO:BP | organic acid metabolic process | 944 | 11 |
| GO:BP | cellular amino acid metabolic process | 253 | 7 |
| GO:BP | small molecule metabolic process | 1713 | 13 |
| GO:BP | cellular modified amino acid metabolic process | 179 | 5 |
| GO:BP | response to copper ion | 33 | 3 |
| GO:BP | hormone metabolic process | 219 | 5 |
| GO:BP | stress response to copper ion | 6 | 2 |
| GO:BP | detoxification of copper ion | 6 | 2 |
| GO:BP | detoxification | 123 | 4 |
| GO:BP | transition metal ion homeostasis | 136 | 4 |
| GO:BP | detoxification of inorganic compound | 9 | 2 |
| GO:BP | stress response to metal ion | 11 | 2 |
| GO:BP | alpha-amino acid metabolic process | 182 | 4 |
| GO:BP | obsolete oxidation-reduction process | 548 | 6 |
| GO:BP | cellular response to zinc ion | 15 | 2 |
| GO:BP | NAD biosynthetic process | 16 | 2 |
| GO:BP | nicotinamide nucleotide biosynthetic process | 20 | 2 |
| GO:BP | pyridine nucleotide biosynthetic process | 20 | 2 |
| GO:BP | carboxylic acid catabolic process | 221 | 4 |
| GO:BP | cellular response to copper ion | 20 | 2 |
| GO:BP | organic acid catabolic process | 228 | 4 |
| GO:BP | response to toxic substance | 240 | 4 |
| GO:BP | pyridine-containing compound biosynthetic process | 23 | 2 |
| GO:BP | cellular transition metal ion homeostasis | 109 | 3 |
| GO:BP | metal ion homeostasis | 685 | 6 |
| GO:BP | nitric oxide mediated signal transduction | 26 | 2 |
| GO:BP | thyroid hormone metabolic process | 27 | 2 |
| GO:BP | cellular zinc ion homeostasis | 28 | 2 |
| GO:BP | pyridine nucleotide metabolic process | 29 | 2 |
| GO:BP | nicotinamide nucleotide metabolic process | 29 | 2 |
| GO:BP | aromatic amino acid family metabolic process | 30 | 2 |
| GO:BP | zinc ion homeostasis | 30 | 2 |
| GO:BP | carboxylic acid biosynthetic process | 282 | 4 |
| GO:BP | pyridine-containing compound metabolic process | 33 | 2 |
| GO:BP | cation homeostasis | 755 | 6 |
| GO:BP | cellular response to cadmium ion | 33 | 2 |
| GO:BP | organic acid biosynthetic process | 290 | 4 |
| GO:BP | response to D-galactose | 1 | 1 |
| GO:BP | iron ion export across plasma membrane | 1 | 1 |
| GO:BP | inorganic ion homeostasis | 768 | 6 |
| GO:BP | N-acetylmannosamine metabolic process | 1 | 1 |
| GO:BP | spleen trabecula formation | 1 | 1 |
| GO:BP | mannosamine metabolic process | 1 | 1 |
| GO:MF | oxidoreductase activity | 815 | 9 |
| GO:MF | hormone binding | 85 | 3 |
| GO:MF | steroid hormone receptor activity | 18 | 2 |
| GO:MF | catalytic activity | 5665 | 18 |
| GO:MF | argininosuccinate lyase activity | 1 | 1 |
| GO:MF | arylformamidase activity | 1 | 1 |
| GO:MF | butyryl-CoA dehydrogenase activity | 2 | 1 |
| GO:MF | iodide peroxidase activity | 2 | 1 |
| GO:MF | malic enzyme activity | 3 | 1 |
| GO:MF | malate dehydrogenase (decarboxylating) (NAD+) activity | 3 | 1 |
| GO:MF | malate dehydrogenase (decarboxylating) (NADP+) activity | 3 | 1 |
| GO:MF | nicotinate-nucleotide diphosphorylase (carboxylating) activity | 3 | 1 |
| GO:MF | thyroxine 5’-deiodinase activity | 3 | 1 |
| GO:MF | oxidoreductase activity, acting on phosphorus or arsenic in donors | 2 | 1 |
| GO:MF | isovaleryl-CoA dehydrogenase activity | 1 | 1 |
| GO:MF | oxidoreductase activity, acting on phosphorus or arsenic in donors, disulfide as acceptor | 2 | 1 |
| GO:MF | glutathione dehydrogenase (ascorbate) activity | 2 | 1 |
| GO:MF | type 1 metabotropic glutamate receptor binding | 2 | 1 |
| GO:MF | thyroxine 5-deiodinase activity | 3 | 1 |
| GO:MF | hormone-sensitive lipase activity | 2 | 1 |
| GO:MF | estrogen response element binding | 3 | 1 |
| GO:MF | triglyceride binding | 3 | 1 |
| GO:MF | oxidoreductase activity, acting on a sulfur group of donors, quinone or similar compound as acceptor | 3 | 1 |
| GO:MF | acireductone dioxygenase [iron(II)-requiring] activity | 1 | 1 |
| GO:MF | transition metal ion binding | 1064 | 7 |
| GO:MF | cysteine-S-conjugate N-acetyltransferase activity | 1 | 1 |
| GO:MF | fructose transmembrane transporter activity | 3 | 1 |
| GO:MF | N-acylglucosamine 2-epimerase activity | 1 | 1 |
| GO:MF | methylarsonate reductase activity | 2 | 1 |
| GO:MF | all-trans-retinol 13,14-reductase activity | 1 | 1 |
| GO:MF | oxidoreductase activity, acting on the CH-CH group of donors, with a flavin as acceptor | 3 | 1 |
| GO:MF | oxidoreductase activity, acting on the CH-CH group of donors | 60 | 2 |
| GO:MF | nicotinamide phosphoribosyltransferase activity | 1 | 1 |
| GO:MF | copper ion binding | 65 | 2 |
| GO:MF | TFIIB-class transcription factor binding | 4 | 1 |
| GO:MF | N-acetyl-beta-D-galactosaminidase activity | 4 | 1 |
| GO:MF | acetylesterase activity | 4 | 1 |
| GO:MF | ferrous iron transmembrane transporter activity | 4 | 1 |
| GO:MF | glutathione disulfide oxidoreductase activity | 4 | 1 |
| GO:MF | oxaloacetate decarboxylase activity | 4 | 1 |
| GO:MF | hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides | 77 | 2 |
| GO:MF | estrogen receptor activity | 5 | 1 |
| GO:MF | aminoacylase activity | 5 | 1 |
| GO:MF | short-chain carboxylesterase activity | 5 | 1 |
| KEGG | Mineral absorption | 53 | 3 |
2.2.10 Functional Enrichment - Liver-specific Ahr Regulated
kable(Diff_Liver_Ahr_PathwayEnrichment$result %>% dplyr::select(source, term_name, term_size, intersection_size),
table.attr = "class=\"striped\"", format = "html")| source | term_name | term_size | intersection_size |
|---|---|---|---|
| GO:BP | small molecule metabolic process | 1713 | 120 |
| GO:BP | organic acid metabolic process | 944 | 81 |
| GO:BP | carboxylic acid metabolic process | 896 | 77 |
| GO:BP | oxoacid metabolic process | 908 | 77 |
| GO:BP | monocarboxylic acid metabolic process | 616 | 55 |
| GO:BP | lipid metabolic process | 1344 | 79 |
| GO:BP | metabolic process | 11429 | 304 |
| GO:BP | cellular lipid metabolic process | 994 | 60 |
| GO:BP | small molecule biosynthetic process | 617 | 46 |
| GO:BP | fatty acid metabolic process | 425 | 37 |
| GO:BP | cellular catabolic process | 2059 | 91 |
| GO:BP | organic acid biosynthetic process | 290 | 30 |
| GO:BP | catabolic process | 2399 | 100 |
| GO:BP | obsolete oxidation-reduction process | 548 | 41 |
| GO:BP | cellular metabolic process | 10350 | 276 |
| GO:BP | alpha-amino acid metabolic process | 182 | 23 |
| GO:BP | carboxylic acid catabolic process | 221 | 25 |
| GO:BP | carboxylic acid biosynthetic process | 282 | 28 |
| GO:BP | small molecule catabolic process | 346 | 31 |
| GO:BP | organic acid catabolic process | 228 | 25 |
| GO:BP | cellular amino acid metabolic process | 253 | 26 |
| GO:BP | organonitrogen compound metabolic process | 6326 | 190 |
| GO:BP | cellular amino acid catabolic process | 92 | 16 |
| GO:BP | organic substance catabolic process | 1985 | 83 |
| GO:BP | organic substance metabolic process | 10989 | 283 |
| GO:BP | hormone metabolic process | 219 | 22 |
| GO:BP | alpha-amino acid catabolic process | 80 | 14 |
| GO:BP | response to hormone | 912 | 48 |
| GO:BP | carbohydrate derivative metabolic process | 975 | 49 |
| GO:BP | organic hydroxy compound metabolic process | 527 | 33 |
| GO:BP | generation of precursor metabolites and energy | 446 | 30 |
| GO:BP | regulation of hormone levels | 559 | 34 |
| GO:BP | cellular hormone metabolic process | 135 | 16 |
| GO:BP | steroid metabolic process | 306 | 24 |
| GO:BP | response to oxygen-containing compound | 1820 | 71 |
| GO:BP | sulfur compound metabolic process | 317 | 24 |
| GO:BP | organophosphate metabolic process | 891 | 44 |
| GO:BP | lipid biosynthetic process | 647 | 36 |
| GO:BP | alpha-amino acid biosynthetic process | 62 | 11 |
| GO:BP | response to endogenous stimulus | 1619 | 65 |
| GO:BP | primary metabolic process | 10243 | 256 |
| GO:BP | alcohol metabolic process | 344 | 24 |
| GO:BP | regulation of biological quality | 3876 | 119 |
| GO:BP | regulation of lipid metabolic process | 361 | 24 |
| GO:BP | triglyceride metabolic process | 112 | 13 |
| GO:BP | monocarboxylic acid biosynthetic process | 194 | 17 |
| GO:BP | organic substance transport | 2416 | 83 |
| GO:BP | unsaturated fatty acid metabolic process | 133 | 14 |
| GO:BP | localization | 6168 | 169 |
| GO:BP | transport | 4502 | 132 |
| GO:BP | response to organonitrogen compound | 1093 | 47 |
| GO:BP | cellular modified amino acid metabolic process | 179 | 16 |
| GO:BP | establishment of localization | 4658 | 135 |
| GO:BP | response to external stimulus | 2912 | 94 |
| GO:BP | carbohydrate metabolic process | 587 | 31 |
| GO:BP | drug metabolic process | 68 | 10 |
| GO:BP | protein catabolic process in the vacuole | 18 | 6 |
| GO:BP | acylglycerol metabolic process | 143 | 14 |
| GO:BP | neutral lipid metabolic process | 145 | 14 |
| GO:BP | nucleobase-containing small molecule metabolic process | 537 | 29 |
| GO:BP | response to nitrogen compound | 1199 | 49 |
| GO:BP | cellular ketone metabolic process | 213 | 17 |
| GO:BP | monosaccharide metabolic process | 266 | 19 |
| GO:BP | response to wounding | 517 | 28 |
| GO:BP | response to drug | 459 | 26 |
| GO:BP | response to stress | 3817 | 114 |
| GO:BP | liver development | 173 | 15 |
| GO:BP | response to organic cyclic compound | 1043 | 44 |
| GO:BP | positive regulation of lipid metabolic process | 174 | 15 |
| GO:BP | hexose metabolic process | 247 | 18 |
| GO:BP | hepaticobiliary system development | 176 | 15 |
| GO:BP | liver morphogenesis | 32 | 7 |
| GO:BP | regulation of small molecule metabolic process | 355 | 22 |
| GO:BP | ribose phosphate metabolic process | 385 | 23 |
| GO:BP | long-chain fatty acid metabolic process | 115 | 12 |
| GO:BP | organonitrogen compound biosynthetic process | 1570 | 58 |
| GO:BP | monosaccharide biosynthetic process | 96 | 11 |
| GO:BP | nucleoside phosphate metabolic process | 476 | 26 |
| GO:BP | cellular amino acid biosynthetic process | 62 | 9 |
| GO:BP | phosphate-containing compound metabolic process | 2809 | 89 |
| GO:BP | organonitrogen compound catabolic process | 1249 | 49 |
| GO:BP | cellular carbohydrate metabolic process | 310 | 20 |
| GO:BP | regulation of hydrolase activity | 1183 | 47 |
| GO:BP | response to organic substance | 3418 | 103 |
| GO:BP | phosphorus metabolic process | 2832 | 89 |
| GO:BP | tyrosine metabolic process | 14 | 5 |
| GO:BP | regulation of inflammatory response | 347 | 21 |
| GO:BP | cellular process | 17828 | 383 |
| GO:BP | aspartate family amino acid catabolic process | 15 | 5 |
| GO:BP | wound healing | 380 | 22 |
| GO:BP | cellular response to hormone stimulus | 600 | 29 |
| GO:BP | cellular response to chemical stimulus | 3097 | 94 |
| GO:BP | lysosomal protein catabolic process | 16 | 5 |
| GO:BP | regulation of peptidase activity | 480 | 25 |
| GO:BP | macromolecule localization | 2897 | 89 |
| GO:BP | gland development | 513 | 26 |
| GO:BP | lipid catabolic process | 335 | 20 |
| GO:BP | regulation of glucose metabolic process | 133 | 12 |
| GO:BP | dicarboxylic acid metabolic process | 92 | 10 |
| GO:BP | regulation of multicellular organismal process | 2788 | 86 |
| GO:BP | aspartate family amino acid metabolic process | 43 | 7 |
| GO:BP | nitrogen compound transport | 1986 | 66 |
| GO:BP | regulation of cell population proliferation | 1753 | 60 |
| GO:BP | nucleotide metabolic process | 466 | 24 |
| GO:BP | ribonucleotide metabolic process | 376 | 21 |
| GO:BP | aromatic amino acid family metabolic process | 30 | 6 |
| GO:BP | cellular amide metabolic process | 1077 | 42 |
| GO:BP | glucose metabolic process | 212 | 15 |
| GO:BP | hepatocyte proliferation | 30 | 6 |
| GO:BP | epithelial cell proliferation involved in liver morphogenesis | 30 | 6 |
| GO:BP | organophosphate biosynthetic process | 500 | 25 |
| GO:BP | secondary alcohol metabolic process | 141 | 12 |
| GO:BP | response to steroid hormone | 352 | 20 |
| GO:BP | mammary gland epithelial cell proliferation | 31 | 6 |
| GO:BP | regulation of cellular carbohydrate metabolic process | 167 | 13 |
| GO:BP | response to lipid | 980 | 39 |
| GO:BP | gland morphogenesis | 144 | 12 |
| GO:BP | cell death | 2136 | 69 |
| GO:BP | regulation of developmental process | 2591 | 80 |
| GO:BP | nitric oxide metabolic process | 82 | 9 |
| GO:BP | olefinic compound metabolic process | 124 | 11 |
| GO:BP | regulation of endopeptidase activity | 451 | 23 |
| GO:BP | response to peptide hormone | 452 | 23 |
| GO:BP | regulation of response to stress | 1254 | 46 |
| GO:BP | reactive nitrogen species metabolic process | 84 | 9 |
| GO:BP | homeostatic process | 1922 | 63 |
| GO:BP | cellular response to xenobiotic stimulus | 106 | 10 |
| GO:BP | response to nutrient levels | 523 | 25 |
| GO:BP | cholesterol metabolic process | 129 | 11 |
| GO:BP | response to extracellular stimulus | 559 | 26 |
| GO:BP | pigment metabolic process | 68 | 8 |
| GO:BP | regulation of response to external stimulus | 904 | 36 |
| GO:BP | response to peptide | 531 | 25 |
| GO:BP | regeneration | 232 | 15 |
| GO:BP | glutathione metabolic process | 70 | 8 |
| GO:BP | arachidonic acid metabolic process | 70 | 8 |
| GO:BP | icosanoid metabolic process | 134 | 11 |
| GO:BP | regulation of protein exit from endoplasmic reticulum | 23 | 5 |
| GO:BP | primary alcohol metabolic process | 90 | 9 |
| GO:BP | hexose biosynthetic process | 90 | 9 |
| GO:BP | positive regulation of inflammatory response | 134 | 11 |
| GO:BP | carbohydrate biosynthetic process | 209 | 14 |
| GO:BP | positive regulation of lipid biosynthetic process | 91 | 9 |
| GO:BP | animal organ regeneration | 91 | 9 |
| GO:BP | glycerolipid metabolic process | 384 | 20 |
| GO:BP | fatty acid oxidation | 114 | 10 |
| GO:BP | sterol metabolic process | 137 | 11 |
| GO:BP | response to nutrient | 187 | 13 |
| GO:BP | response to xenobiotic stimulus | 115 | 10 |
| GO:BP | transmembrane transport | 1533 | 52 |
| GO:BP | purine ribonucleotide metabolic process | 358 | 19 |
| GO:BP | positive regulation of response to wounding | 74 | 8 |
| GO:BP | triglyceride biosynthetic process | 39 | 6 |
| GO:BP | glomerular filtration | 25 | 5 |
| GO:BP | regulation of cell death | 1740 | 57 |
| GO:BP | cellular response to nutrient levels | 217 | 14 |
| GO:BP | regulation of response to wounding | 165 | 12 |
| GO:BP | positive regulation of hydrolase activity | 653 | 28 |
| GO:BP | cell population proliferation | 2072 | 65 |
| GO:BP | complement activation, alternative pathway | 14 | 4 |
| GO:BP | regulation of body fluid levels | 364 | 19 |
| GO:BP | organic cyclic compound catabolic process | 458 | 22 |
| GO:BP | lipid oxidation | 120 | 10 |
| GO:BP | renal filtration | 26 | 5 |
| GO:BP | nitric oxide biosynthetic process | 77 | 8 |
| GO:BP | pyruvate biosynthetic process | 6 | 3 |
| GO:BP | inflammatory response | 732 | 30 |
| GO:BP | monocarboxylic acid catabolic process | 122 | 10 |
| GO:BP | cellular response to extracellular stimulus | 252 | 15 |
| GO:BP | protein exit from endoplasmic reticulum | 42 | 6 |
| GO:BP | cellular response to endogenous stimulus | 1333 | 46 |
| GO:BP | regulation of carbohydrate metabolic process | 199 | 13 |
| GO:BP | programmed cell death | 1975 | 62 |
| GO:BP | purine-containing compound metabolic process | 406 | 20 |
| GO:BP | regulation of proteolysis | 778 | 31 |
| GO:BP | xenobiotic metabolic process | 102 | 9 |
| GO:BP | secondary metabolic process | 61 | 7 |
| GO:BP | cellular response to nitrogen compound | 710 | 29 |
| GO:BP | regulation of wound healing | 126 | 10 |
| GO:BP | response to glucocorticoid | 176 | 12 |
| GO:BP | negative regulation of proteolysis | 379 | 19 |
| GO:BP | cellular response to organonitrogen compound | 643 | 27 |
| GO:BP | regulation of defense response | 575 | 25 |
| GO:BP | aromatic amino acid family catabolic process | 16 | 4 |
| GO:BP | nucleoside phosphate biosynthetic process | 232 | 14 |
| GO:BP | positive regulation of steroid hormone biosynthetic process | 7 | 3 |
| GO:BP | cellular response to external stimulus | 322 | 17 |
| GO:BP | nitrogen compound metabolic process | 9669 | 227 |
| GO:BP | protein-containing complex subunit organization | 1636 | 53 |
| GO:BP | purine nucleotide metabolic process | 385 | 19 |
| GO:BP | cellular response to oxygen-containing compound | 1247 | 43 |
| GO:BP | regulation of phagocytosis | 108 | 9 |
| GO:BP | transmembrane receptor protein tyrosine kinase signaling pathway | 587 | 25 |
| GO:BP | glycosyl compound metabolic process | 86 | 8 |
| GO:BP | regulation of immune system process | 1406 | 47 |
| GO:BP | regulation of epithelial cell proliferation | 359 | 18 |
| GO:BP | intracellular transport | 1409 | 47 |
| GO:BP | response to gonadotropin | 31 | 5 |
| GO:BP | gluconeogenesis | 87 | 8 |
| GO:BP | glutamate metabolic process | 31 | 5 |
| GO:BP | acylglycerol biosynthetic process | 48 | 6 |
| GO:BP | neutral lipid biosynthetic process | 48 | 6 |
| GO:BP | regulation of cysteine-type endopeptidase activity involved in apoptotic process | 214 | 13 |
| GO:BP | cellular lipid catabolic process | 214 | 13 |
| GO:BP | lipid localization | 459 | 21 |
| GO:BP | ketone catabolic process | 18 | 4 |
| GO:BP | steroid biosynthetic process | 161 | 11 |
| GO:BP | positive regulation of response to stimulus | 2198 | 66 |
| GO:BP | protein-containing complex assembly | 1462 | 48 |
| GO:BP | malate metabolic process | 8 | 3 |
| GO:BP | erythrose 4-phosphate/phosphoenolpyruvate family amino acid catabolic process | 8 | 3 |
| GO:BP | sarcosine metabolic process | 2 | 2 |
| GO:BP | xenobiotic detoxification by transmembrane export across the plasma membrane | 8 | 3 |
| GO:BP | L-phenylalanine catabolic process | 8 | 3 |
| GO:BP | biosynthetic process | 5882 | 148 |
| GO:BP | aromatic compound catabolic process | 432 | 20 |
| GO:BP | regulation of programmed cell death | 1587 | 51 |
| GO:BP | pyruvate metabolic process | 114 | 9 |
| GO:BP | negative regulation of cell death | 1119 | 39 |
| GO:BP | negative regulation of endopeptidase activity | 278 | 15 |
| GO:BP | endoplasmic reticulum tubular network organization | 19 | 4 |
| GO:BP | regulation of mammary gland epithelial cell proliferation | 19 | 4 |
| GO:BP | organic anion transport | 372 | 18 |
| GO:BP | negative regulation of cellular process | 5068 | 130 |
| GO:BP | retinoid metabolic process | 71 | 7 |
| GO:BP | response to corticosteroid | 194 | 12 |
| GO:BP | lipid homeostasis | 167 | 11 |
| GO:BP | bile acid and bile salt transport | 34 | 5 |
| GO:BP | negative regulation of protein metabolic process | 1128 | 39 |
| GO:BP | negative regulation of biological process | 5544 | 140 |
| GO:BP | regulation of triglyceride metabolic process | 52 | 6 |
| GO:BP | response to stilbenoid | 20 | 4 |
| GO:BP | regulation of cell differentiation | 1649 | 52 |
| GO:BP | development of secondary female sexual characteristics | 9 | 3 |
| GO:BP | L-phenylalanine metabolic process | 9 | 3 |
| GO:BP | regulation of response to stimulus | 3851 | 103 |
| GO:BP | mammary gland development | 170 | 11 |
| GO:BP | epithelial fluid transport | 9 | 3 |
| GO:BP | erythrose 4-phosphate/phosphoenolpyruvate family amino acid metabolic process | 9 | 3 |
| GO:BP | regulation of ERBB signaling pathway | 73 | 7 |
| GO:BP | ion transport | 1572 | 50 |
| GO:BP | positive regulation of defense response | 256 | 14 |
| GO:BP | protein transport | 1535 | 49 |
| GO:BP | negative regulation of peptidase activity | 287 | 15 |
| GO:BP | response to oxidative stress | 447 | 20 |
| GO:BP | regulation of protein-containing complex assembly | 448 | 20 |
| GO:BP | protein homotetramerization | 54 | 6 |
| GO:BP | quinone metabolic process | 36 | 5 |
| GO:BP | positive regulation of ERBB signaling pathway | 36 | 5 |
| GO:BP | temperature homeostasis | 173 | 11 |
| GO:BP | system development | 4876 | 125 |
| GO:BP | defense response | 1705 | 53 |
| GO:BP | negative regulation of cellular protein metabolic process | 1068 | 37 |
| GO:BP | enzyme linked receptor protein signaling pathway | 916 | 33 |
| GO:BP | positive regulation of wound healing | 55 | 6 |
| GO:BP | ribose phosphate biosynthetic process | 175 | 11 |
| GO:BP | positive regulation of phagocytosis | 76 | 7 |
| GO:BP | porphyrin-containing compound metabolic process | 37 | 5 |
| GO:BP | serine family amino acid metabolic process | 37 | 5 |
| GO:BP | regulation of fatty acid metabolic process | 99 | 8 |
| GO:BP | fatty acid catabolic process | 99 | 8 |
| GO:BP | positive regulation of biological process | 6305 | 155 |
| GO:BP | positive regulation of sister chromatid cohesion | 10 | 3 |
| GO:BP | diterpenoid metabolic process | 77 | 7 |
| GO:BP | regulation of fatty acid beta-oxidation | 22 | 4 |
| GO:BP | regulation of hepatocyte proliferation | 22 | 4 |
| GO:BP | negative regulation of cell maturation | 10 | 3 |
| GO:BP | negative regulation of hydrolase activity | 457 | 20 |
| GO:BP | epithelial cell proliferation | 424 | 19 |
| GO:BP | NADP metabolic process | 38 | 5 |
| GO:BP | fatty acid biosynthetic process | 151 | 10 |
| GO:BP | macrophage migration | 57 | 6 |
| GO:BP | regulation of cysteine-type endopeptidase activity | 237 | 13 |
| GO:BP | protein localization | 2452 | 70 |
| GO:BP | response to toxic substance | 240 | 13 |
| GO:BP | response to estradiol | 155 | 10 |
| GO:BP | regulation of renal system process | 40 | 5 |
| GO:BP | xenobiotic transport | 40 | 5 |
| GO:BP | negative regulation of cell population proliferation | 715 | 27 |
| GO:BP | cellular response to drug | 81 | 7 |
| GO:BP | low-density lipoprotein particle mediated signaling | 3 | 2 |
| GO:BP | lipoprotein particle mediated signaling | 3 | 2 |
| GO:BP | fumarate metabolic process | 3 | 2 |
| GO:BP | isoleucine biosynthetic process | 3 | 2 |
| GO:BP | chylomicron remodeling | 3 | 2 |
| GO:BP | regulation of platelet-derived growth factor receptor signaling pathway | 24 | 4 |
| GO:BP | protein tetramerization | 82 | 7 |
| GO:BP | cellular response to peptide | 370 | 17 |
| GO:BP | apoptotic process | 1919 | 57 |
| GO:BP | regulation of lipid biosynthetic process | 187 | 11 |
| GO:BP | regulation of localization | 2868 | 79 |
| GO:BP | cellular response to peptide hormone stimulus | 309 | 15 |
| GO:BP | regulation of apoptotic process | 1550 | 48 |
| GO:BP | C21-steroid hormone metabolic process | 42 | 5 |
| GO:BP | one-carbon metabolic process | 42 | 5 |
| GO:BP | lipid modification | 218 | 12 |
| GO:BP | positive regulation of small molecule metabolic process | 161 | 10 |
| GO:BP | terpenoid metabolic process | 85 | 7 |
| GO:BP | CDP-diacylglycerol biosynthetic process | 12 | 3 |
| GO:BP | regulation of glomerular filtration | 12 | 3 |
| GO:BP | positive regulation of hormone biosynthetic process | 12 | 3 |
| GO:BP | development of secondary sexual characteristics | 12 | 3 |
| GO:BP | multicellular organism development | 5441 | 135 |
| GO:BP | hormone biosynthetic process | 63 | 6 |
| GO:BP | renal system process involved in regulation of systemic arterial blood pressure | 26 | 4 |
| GO:BP | response to chemical | 5544 | 137 |
| GO:BP | establishment of protein localization | 1647 | 50 |
| GO:BP | regulation of blood coagulation | 64 | 6 |
| GO:BP | regulation of gluconeogenesis | 64 | 6 |
| GO:BP | positive regulation of transport | 1005 | 34 |
| GO:BP | establishment of localization in cell | 2031 | 59 |
| GO:BP | chemical homeostasis | 1245 | 40 |
| GO:BP | lipid storage | 88 | 7 |
| GO:BP | anatomical structure development | 5987 | 146 |
| GO:BP | estrogen metabolic process | 27 | 4 |
| GO:BP | regulation of cell maturation | 27 | 4 |
| GO:BP | renal system process | 113 | 8 |
| GO:BP | CDP-diacylglycerol metabolic process | 13 | 3 |
| GO:BP | alditol phosphate metabolic process | 13 | 3 |
| GO:BP | positive regulation of nuclear-transcribed mRNA poly(A) tail shortening | 13 | 3 |
| GO:BP | formation of translation preinitiation complex | 13 | 3 |
| GO:BP | response to folic acid | 13 | 3 |
| GO:BP | dicarboxylic acid biosynthetic process | 13 | 3 |
| GO:BP | fructose metabolic process | 13 | 3 |
| GO:BP | positive regulation of protein exit from endoplasmic reticulum | 13 | 3 |
| GO:BP | energy reserve metabolic process | 89 | 7 |
| GO:BP | regulation of hemostasis | 66 | 6 |
| GO:BP | regulation of transport | 1871 | 55 |
| GO:BP | small GTPase mediated signal transduction | 422 | 18 |
| GO:BP | tetrapyrrole metabolic process | 46 | 5 |
| GO:BP | positive regulation of fatty acid metabolic process | 46 | 5 |
| GO:BP | regulation of coagulation | 67 | 6 |
| GO:BP | regulation of nitric oxide biosynthetic process | 67 | 6 |
| GO:BP | nucleotide biosynthetic process | 229 | 12 |
| GO:BP | anion transport | 529 | 21 |
| GO:BP | endoplasmic reticulum tubular network membrane organization | 4 | 2 |
| GO:BP | negative regulation of dendritic cell differentiation | 4 | 2 |
| GO:BP | regulation of epidermal growth factor receptor signaling pathway | 68 | 6 |
| GO:BP | response to hypoxia | 326 | 15 |
| GO:BP | heme catabolic process | 4 | 2 |
| GO:BP | L-ascorbic acid biosynthetic process | 4 | 2 |
| GO:BP | response to 2,3,7,8-tetrachlorodibenzodioxine | 4 | 2 |
| GO:BP | endoplasmic reticulum tubular network formation | 4 | 2 |
| GO:BP | porphyrin-containing compound catabolic process | 4 | 2 |
| GO:BP | NADP biosynthetic process | 4 | 2 |
| GO:BP | L-kynurenine catabolic process | 4 | 2 |
| GO:BP | regulation of erythrocyte differentiation | 47 | 5 |
| GO:BP | pigment catabolic process | 4 | 2 |
| GO:BP | retinol metabolic process | 47 | 5 |
| GO:BP | organic substance biosynthetic process | 5779 | 141 |
| GO:BP | regulation of carbohydrate biosynthetic process | 117 | 8 |
| GO:BP | organic acid transport | 327 | 15 |
| GO:BP | regulation of nuclear-transcribed mRNA poly(A) tail shortening | 14 | 3 |
| GO:BP | growth hormone receptor signaling pathway | 14 | 3 |
| GO:BP | positive regulation of immune system process | 947 | 32 |
| GO:BP | aldehyde catabolic process | 14 | 3 |
| GO:BP | positive regulation of molecular function | 1678 | 50 |
| GO:BP | response to lipoprotein particle | 29 | 4 |
| GO:BP | regulation of nitric oxide metabolic process | 69 | 6 |
| GO:BP | regulation of interleukin-1 beta production | 93 | 7 |
| GO:BP | positive regulation of multicellular organismal process | 1555 | 47 |
| GO:BP | interleukin-1 beta production | 93 | 7 |
| GO:BP | positive regulation of catalytic activity | 1268 | 40 |
| GO:BP | immune effector process | 683 | 25 |
| GO:BP | carboxylic acid transport | 297 | 14 |
| GO:BP | carbohydrate derivative biosynthetic process | 574 | 22 |
| GO:BP | vitamin metabolic process | 70 | 6 |
| GO:BP | acyl-CoA metabolic process | 94 | 7 |
| GO:BP | thioester metabolic process | 94 | 7 |
| GO:BP | animal organ development | 3617 | 94 |
| GO:BP | energy derivation by oxidation of organic compounds | 300 | 14 |
| GO:BP | fluid transport | 30 | 4 |
| GO:BP | exogenous drug catabolic process | 49 | 5 |
| GO:BP | glutamine family amino acid metabolic process | 71 | 6 |
| GO:BP | negative regulation of circadian rhythm | 15 | 3 |
| GO:BP | regulation of cholesterol storage | 15 | 3 |
| GO:BP | renal system process involved in regulation of blood volume | 15 | 3 |
| GO:BP | regulation of NLRP3 inflammasome complex assembly | 15 | 3 |
| GO:BP | branched-chain amino acid metabolic process | 15 | 3 |
| GO:BP | developmental process | 6536 | 156 |
| GO:BP | cellular localization | 2777 | 75 |
| GO:BP | glucan metabolic process | 72 | 6 |
| GO:BP | cellular glucan metabolic process | 72 | 6 |
| GO:BP | drug catabolic process | 50 | 5 |
| GO:BP | glycogen metabolic process | 72 | 6 |
| GO:BP | positive regulation of response to external stimulus | 404 | 17 |
| GO:BP | negative regulation of programmed cell death | 1002 | 33 |
| GO:BP | positive regulation of protein-containing complex assembly | 240 | 12 |
| GO:BP | response to growth hormone | 31 | 4 |
| GO:BP | heme metabolic process | 31 | 4 |
| GO:BP | detoxification | 123 | 8 |
| GO:BP | mammary gland epithelium development | 73 | 6 |
| GO:BP | regulation of lipase activity | 73 | 6 |
| GO:BP | positive regulation of cell population proliferation | 1045 | 34 |
| GO:BP | regulation of immune effector process | 339 | 15 |
| GO:BP | alcohol catabolic process | 51 | 5 |
| GO:BP | cellular component organization or biogenesis | 6270 | 150 |
| GO:BP | organic hydroxy compound catabolic process | 74 | 6 |
| GO:BP | response to decreased oxygen levels | 341 | 15 |
| GO:BP | cellular response to lipoprotein particle stimulus | 32 | 4 |
| GO:BP | Golgi to endosome transport | 16 | 3 |
| GO:BP | glycine metabolic process | 16 | 3 |
| GO:BP | regulation of lysosome organization | 5 | 2 |
| GO:BP | negative regulation of oocyte maturation | 5 | 2 |
| GO:BP | regulation of cellular response to insulin stimulus | 75 | 6 |
| GO:BP | omega-hydroxylase P450 pathway | 5 | 2 |
| GO:BP | purine-containing compound biosynthetic process | 184 | 10 |
| GO:BP | epithelial cell proliferation involved in mammary gland duct elongation | 5 | 2 |
| GO:BP | mammary gland branching involved in thelarche | 5 | 2 |
| GO:BP | positive regulation of small GTPase mediated signal transduction | 75 | 6 |
| GO:BP | cellular nitrogen compound catabolic process | 411 | 17 |
| GO:BP | long-chain fatty acid catabolic process | 5 | 2 |
| GO:BP | thelarche | 5 | 2 |
| GO:BP | triglyceride transport | 5 | 2 |
| GO:BP | acylglycerol transport | 5 | 2 |
| GO:BP | tetrapyrrole catabolic process | 5 | 2 |
| GO:BP | canalicular bile acid transport | 5 | 2 |
| GO:BP | positive regulation of platelet-derived growth factor receptor signaling pathway | 5 | 2 |
| GO:BP | branched-chain amino acid biosynthetic process | 5 | 2 |
| GO:BP | cellular component organization | 6090 | 146 |
| GO:CC | cytoplasm | 11093 | 318 |
| GO:CC | organelle membrane | 3076 | 135 |
| GO:CC | endoplasmic reticulum | 1761 | 83 |
| GO:CC | endoplasmic reticulum membrane | 993 | 58 |
| GO:CC | organelle subcompartment | 1580 | 77 |
| GO:CC | endoplasmic reticulum subcompartment | 999 | 58 |
| GO:CC | intracellular anatomical structure | 14111 | 349 |
| GO:CC | nuclear outer membrane-endoplasmic reticulum membrane network | 1018 | 58 |
| GO:CC | endomembrane system | 4006 | 141 |
| GO:CC | mitochondrion | 1827 | 80 |
| GO:CC | mitochondrial membrane | 677 | 41 |
| GO:CC | envelope | 1176 | 57 |
| GO:CC | organelle envelope | 1176 | 57 |
| GO:CC | mitochondrial envelope | 736 | 42 |
| GO:CC | intracellular membrane-bounded organelle | 11363 | 287 |
| GO:CC | membrane-bounded organelle | 11812 | 292 |
| GO:CC | mitochondrial inner membrane | 451 | 29 |
| GO:CC | cellular anatomical entity | 19567 | 416 |
| GO:CC | organelle inner membrane | 510 | 29 |
| GO:CC | intracellular organelle | 12510 | 300 |
| GO:CC | organelle | 12827 | 304 |
| GO:CC | apical part of cell | 474 | 26 |
| GO:CC | apical plasma membrane | 388 | 23 |
| GO:CC | endosome membrane | 403 | 22 |
| GO:CC | membrane | 10122 | 244 |
| GO:CC | peroxisome | 148 | 12 |
| GO:CC | microbody | 148 | 12 |
| GO:CC | bounding membrane of organelle | 1676 | 57 |
| GO:CC | Golgi apparatus | 1449 | 51 |
| GO:CC | lytic vacuole | 468 | 23 |
| GO:CC | lysosome | 468 | 23 |
| GO:CC | vacuole | 562 | 26 |
| GO:CC | vacuolar membrane | 280 | 16 |
| GO:CC | vesicle membrane | 833 | 32 |
| GO:CC | cytosol | 3849 | 105 |
| GO:CC | lysosomal membrane | 219 | 13 |
| GO:CC | lytic vacuole membrane | 219 | 13 |
| GO:CC | Golgi apparatus subcompartment | 746 | 29 |
| GO:CC | vesicle | 2077 | 63 |
| GO:CC | plasma membrane region | 1318 | 44 |
| GO:CC | endosome | 870 | 32 |
| GO:CC | basal part of cell | 291 | 15 |
| GO:CC | membrane raft | 392 | 18 |
| GO:CC | membrane microdomain | 393 | 18 |
| GO:CC | microvillus | 106 | 8 |
| GO:CC | cytoplasmic vesicle | 1931 | 58 |
| GO:CC | basal plasma membrane | 272 | 14 |
| GO:CC | intracellular vesicle | 1937 | 58 |
| GO:CC | brush border | 134 | 9 |
| GO:CC | cell surface | 1061 | 35 |
| GO:CC | brush border membrane | 73 | 6 |
| GO:CC | recycling endosome | 179 | 10 |
| GO:CC | endoplasmic reticulum tubular network membrane | 5 | 2 |
| GO:CC | intracellular canaliculus | 5 | 2 |
| GO:CC | caveola | 100 | 7 |
| GO:MF | catalytic activity | 5665 | 208 |
| GO:MF | oxidoreductase activity | 815 | 56 |
| GO:MF | oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen | 217 | 22 |
| GO:MF | monooxygenase activity | 159 | 18 |
| GO:MF | small molecule binding | 2543 | 92 |
| GO:MF | anion binding | 2420 | 89 |
| GO:MF | vitamin binding | 141 | 16 |
| GO:MF | oxidoreductase activity, acting on CH-OH group of donors | 154 | 16 |
| GO:MF | identical protein binding | 2140 | 77 |
| GO:MF | heme binding | 183 | 16 |
| GO:MF | iron ion binding | 211 | 17 |
| GO:MF | oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor | 143 | 14 |
| GO:MF | pyridoxal phosphate binding | 54 | 9 |
| GO:MF | vitamin B6 binding | 55 | 9 |
| GO:MF | ion binding | 5862 | 160 |
| GO:MF | tetrapyrrole binding | 192 | 16 |
| GO:MF | lyase activity | 198 | 16 |
| GO:MF | transaminase activity | 22 | 6 |
| GO:MF | transferase activity, transferring nitrogenous groups | 23 | 6 |
| GO:MF | hydrolase activity | 2353 | 75 |
| GO:MF | nucleoside phosphate binding | 2185 | 70 |
| GO:MF | nucleotide binding | 2185 | 70 |
| GO:MF | transferase activity | 2277 | 72 |
| GO:MF | glutathione transferase activity | 33 | 6 |
| GO:MF | steroid hydroxylase activity | 69 | 8 |
| GO:MF | acyltransferase activity, transferring groups other than amino-acyl groups | 232 | 15 |
| GO:MF | aromatase activity | 36 | 6 |
| GO:MF | acyltransferase activity | 263 | 16 |
| GO:MF | nickel cation binding | 5 | 3 |
| GO:MF | bile acid binding | 13 | 4 |
| GO:MF | magnesium ion binding | 218 | 14 |
| GO:MF | lipid transporter activity | 147 | 11 |
| GO:MF | carboxylic acid binding | 174 | 12 |
| GO:MF | active transmembrane transporter activity | 346 | 18 |
| GO:MF | protein-containing complex binding | 1464 | 49 |
| GO:MF | lipid binding | 786 | 31 |
| GO:MF | 1-acyl-2-lysophosphatidylserine acylhydrolase activity | 7 | 3 |
| GO:MF | phosphatidylserine 1-acylhydrolase activity | 7 | 3 |
| GO:MF | transferase activity, transferring alkyl or aryl (other than methyl) groups | 65 | 7 |
| GO:MF | oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen | 65 | 7 |
| GO:MF | organic hydroxy compound transmembrane transporter activity | 47 | 6 |
| GO:MF | L-threonine ammonia-lyase activity | 2 | 2 |
| GO:MF | flavin adenine dinucleotide binding | 90 | 8 |
| GO:MF | amide binding | 367 | 18 |
| GO:MF | steroid binding | 114 | 9 |
| GO:MF | phospholipase A1 activity | 9 | 3 |
| GO:MF | transition metal ion binding | 1064 | 37 |
| GO:MF | oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen | 54 | 6 |
| GO:MF | monocarboxylic acid transmembrane transporter activity | 56 | 6 |
| GO:MF | ATPase-coupled transmembrane transporter activity | 125 | 9 |
| GO:MF | L-serine ammonia-lyase activity | 3 | 2 |
| GO:MF | long-chain fatty acid omega-hydroxylase activity | 3 | 2 |
| GO:MF | transporter activity | 1137 | 38 |
| GO:MF | bile acid transmembrane transporter activity | 23 | 4 |
| GO:MF | protein binding | 10189 | 233 |
| GO:MF | purine nucleobase binding | 3 | 2 |
| GO:MF | primary active transmembrane transporter activity | 128 | 9 |
| GO:MF | carboxylic ester hydrolase activity | 153 | 10 |
| GO:MF | sphingolipid delta-4 desaturase activity | 3 | 2 |
| GO:MF | pattern recognition receptor activity | 23 | 4 |
| GO:MF | monocarboxylic acid binding | 80 | 7 |
| GO:MF | estrogen 2-hydroxylase activity | 3 | 2 |
| GO:MF | oxidoreductase activity, acting on paired donors, with oxidation of a pair of donors resulting in the reduction of molecular oxygen to two molecules of water | 11 | 3 |
| GO:MF | N-acyltransferase activity | 103 | 8 |
| GO:MF | serine-type peptidase activity | 217 | 12 |
| GO:MF | carbon-sulfur lyase activity | 12 | 3 |
| GO:MF | serine hydrolase activity | 222 | 12 |
| GO:MF | carbohydrate derivative binding | 2248 | 64 |
| GO:MF | alcohol dehydrogenase (NADP+) activity | 27 | 4 |
| GO:MF | organic cyclic compound binding | 5768 | 141 |
| GO:MF | protein homodimerization activity | 676 | 25 |
| GO:MF | sn-1-glycerol-3-phosphate C16:0-DCA-CoA acyl transferase activity | 4 | 2 |
| GO:MF | glycerol-3-phosphate O-acyltransferase activity | 4 | 2 |
| GO:MF | thrombospondin receptor activity | 4 | 2 |
| GO:MF | serine-type endopeptidase activity | 202 | 11 |
| GO:MF | folic acid binding | 14 | 3 |
| GO:MF | retinol binding | 14 | 3 |
| GO:MF | organic acid binding | 145 | 9 |
| GO:MF | ribonucleotide binding | 1937 | 56 |
| GO:MF | steroid dehydrogenase activity | 48 | 5 |
| GO:MF | estrogen receptor binding | 49 | 5 |
| GO:MF | xenobiotic transmembrane transporter activity | 30 | 4 |
| GO:MF | aldo-keto reductase (NADP) activity | 30 | 4 |
| GO:MF | oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced iron-sulfur protein as one donor, and incorporation of one atom of oxygen | 15 | 3 |
| GO:MF | peptide hormone binding | 51 | 5 |
| GO:MF | binding | 14895 | 319 |
| GO:MF | lipase activity | 124 | 8 |
| GO:MF | hydrolase activity, acting on ester bonds | 735 | 26 |
| GO:MF | sodium-independent organic anion transmembrane transporter activity | 16 | 3 |
| GO:MF | nucleobase binding | 5 | 2 |
| GO:MF | carboxylic acid transmembrane transporter activity | 155 | 9 |
| GO:MF | ammonia-lyase activity | 5 | 2 |
| GO:MF | neurotrophin receptor activity | 5 | 2 |
| GO:MF | fatty acid omega-hydroxylase activity | 5 | 2 |
| GO:MF | lipoprotein lipase activity | 5 | 2 |
| GO:MF | oxidoreductase activity, acting on the CH-OH group of donors, oxygen as acceptor | 5 | 2 |
| GO:MF | organic acid transmembrane transporter activity | 156 | 9 |
| HP | Abnormal circulating metabolite concentration | 1099 | 60 |
| HP | Autosomal recessive inheritance | 2708 | 109 |
| HP | Abnormal circulating carboxylic acid concentration | 216 | 22 |
| HP | Abnormality of metabolism/homeostasis | 2240 | 90 |
| HP | Abnormal circulating amino acid concentration | 121 | 13 |
| KEGG | Metabolic pathways | 1563 | 102 |
| KEGG | Bile secretion | 100 | 14 |
| KEGG | Chemical carcinogenesis | 101 | 14 |
| KEGG | Biosynthesis of amino acids | 78 | 11 |
| KEGG | Carbon metabolism | 121 | 13 |
| KEGG | Cholesterol metabolism | 49 | 8 |
| KEGG | Glycine, serine and threonine metabolism | 39 | 7 |
| KEGG | Cysteine and methionine metabolism | 52 | 8 |
| KEGG | Drug metabolism - cytochrome P450 | 71 | 9 |
| KEGG | Pyruvate metabolism | 44 | 7 |
| KEGG | Metabolism of xenobiotics by cytochrome P450 | 73 | 9 |
| KEGG | Complement and coagulation cascades | 92 | 10 |
| KEGG | Lysosome | 131 | 12 |
| KEGG | Glycerophospholipid metabolism | 98 | 10 |
| KEGG | Tyrosine metabolism | 39 | 6 |
| KEGG | Glutathione metabolism | 71 | 8 |
| KEGG | Steroid hormone biosynthesis | 91 | 9 |
| KEGG | Peroxisome | 86 | 8 |
| KEGG | Phenylalanine metabolism | 22 | 4 |
| KEGG | PPAR signaling pathway | 89 | 8 |
| REAC | Metabolism | 1679 | 109 |
| REAC | Metabolism of amino acids and derivatives | 234 | 26 |
| REAC | Metabolism of lipids | 573 | 38 |
| REAC | Phenylalanine and tyrosine metabolism | 10 | 4 |
| REAC | Bile acid and bile salt metabolism | 40 | 7 |
| REAC | Biological oxidations | 204 | 17 |
| REAC | Pyruvate metabolism and Citric Acid (TCA) cycle | 50 | 7 |
| REAC | Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol | 24 | 5 |
| REAC | Metabolism of steroids | 112 | 11 |
| REAC | Glutamate and glutamine metabolism | 13 | 4 |
| REAC | Heme degradation | 14 | 4 |
| REAC | Recycling of bile acids and salts | 14 | 4 |
| TF | Factor: GKLF; motif: NNNRGGNGNGGSN | 15302 | 353 |
| TF | Factor: ZBP89; motif: CCCCKCCCCCNN; match class: 1 | 3885 | 117 |
| TF | Factor: GKLF; motif: NNNRGGNGNGGSN; match class: 1 | 10998 | 267 |
| TF | Factor: Egr-2; motif: GCGTGGGCGG | 7210 | 189 |
| TF | Factor: GKLF; motif: NNRRGRRNGNSNNN | 12950 | 301 |
| TF | Factor: Mxi1; motif: NCACGTGGSNGNNNN | 3073 | 94 |
| TF | Factor: ZF5; motif: NRNGNGCGCGCWN | 14469 | 327 |
| TF | Factor: FOXN4; motif: NNWANNCGWMCGCGTCNNNNMT; match class: 1 | 12768 | 294 |
| TF | Factor: Pax-4; motif: NNNNNYCACCCB | 18716 | 398 |
| TF | Factor: Sp1; motif: GGNGGGGGNGGGGGMGGGGCNGGG | 10752 | 255 |
| TF | Factor: ZF5; motif: GYCGCGCARNGCNN | 9484 | 230 |
| TF | Factor: Kid3; motif: CCACN; match class: 1 | 21165 | 431 |
| TF | Factor: NF-E2; motif: CATGACTCAGCANNCN; match class: 1 | 47 | 7 |
| TF | Factor: ZFP187; motif: NNGMCCTNGTCCNYNN | 2555 | 79 |
| TF | Factor: ZBP89; motif: CCCCKCCCCCNN | 8105 | 201 |
| TF | Factor: E2F-4; motif: NTTTCSCGCC; match class: 1 | 5364 | 143 |
| TF | Factor: SP1:SP3; motif: CCSCCCCCYCC | 6684 | 171 |
| TF | Factor: MAZ; motif: GGGGAGGG | 8416 | 206 |
| TF | Factor: GKLF; motif: NNRRGRRNGNSNNN; match class: 1 | 8470 | 207 |
| TF | Factor: SP1:SP3; motif: CCSCCCCCYCC; match class: 1 | 3378 | 98 |
| TF | Factor: MAZ; motif: NKGGGAGGGGRGGR | 7957 | 197 |
| TF | Factor: E2F-1; motif: GNGGGCGGGRMN | 14228 | 319 |
| TF | Factor: Hes1; motif: NNCACGYGNN; match class: 1 | 11386 | 265 |
| TF | Factor: Klf15; motif: RGGGMGGRGNNGGGGGNGG | 3269 | 95 |
| TF | Factor: BCL6B; motif: NNNNCCGCCCCWNNNN | 13664 | 309 |
| TF | Factor: ZF5; motif: GSGCGCGR | 14821 | 330 |
| TF | Factor: NGFI-C; motif: WTGCGTGGGYGG | 5000 | 133 |
| TF | Factor: WT1; motif: NNGGGNGGGSGN | 7486 | 186 |
| TF | Factor: ZF5; motif: GYCGCGCARNGCNN; match class: 1 | 5819 | 151 |
| TF | Factor: E2F-4; motif: NTTTCSCGCC | 10545 | 248 |
| TF | Factor: Osx; motif: CCNCCCCCNNN | 6158 | 158 |
| TF | Factor: WT1; motif: SMCNCCNSC | 8128 | 199 |
| TF | Factor: PPAR,; motif: RGGNCAAAGGTCA | 2376 | 73 |
| TF | Factor: c-Myc:Max; motif: NNNNNNNCACGTGNNNNNNN | 7236 | 180 |
| TF | Factor: Arnt; motif: NNNNNRTCACGTGAYNNNNN; match class: 1 | 7087 | 177 |
| TF | Factor: PPARgamma:RXR-alpha; motif: NTRGGNCARAGGKCA; match class: 1 | 5253 | 138 |
| TF | Factor: c-Myc:Max; motif: NNNNNNNCACGTGNNNNNNN; match class: 1 | 7236 | 180 |
| TF | Factor: E2F; motif: GGCGSG | 10391 | 244 |
| TF | Factor: Arnt; motif: NNNNNRTCACGTGAYNNNNN | 7087 | 177 |
| TF | Factor: FOXN4; motif: NNWANNCGWMCGCGTCNNNNMT | 16009 | 350 |
| TF | Factor: E2F-4; motif: NGGGGGCGGGRMNN | 6987 | 174 |
| TF | Factor: BEN; motif: CAGCGRNV | 16234 | 353 |
| TF | Factor: CKROX; motif: SCCCTCCCC | 6334 | 160 |
| TF | Factor: E2F-3; motif: GGCGGGN | 11268 | 260 |
| TF | Factor: STAT1; motif: NNNSANTTCCGGGAANTGNSN; match class: 1 | 2881 | 83 |
| TF | Factor: HIF-1alpha; motif: NCACGT | 6382 | 160 |
| TF | Factor: BTEB2; motif: GNAGGGGGNGGGSSNN | 4977 | 130 |
| TF | Factor: MAZ; motif: NKGGGAGGGGRGGR; match class: 1 | 4159 | 112 |
| TF | Factor: c-Myc:Max; motif: NNACCACGTGGTNN; match class: 1 | 7970 | 193 |
| TF | Factor: ARNTLIKE; motif: NNNSCACGTG | 5261 | 136 |
| TF | Factor: c-Myc:Max; motif: NNACCACGTGGTNN | 7970 | 193 |
| TF | Factor: Pax-5; motif: BCNNNRNGCANBGNTGNRTAGCSGCHNB; match class: 1 | 3991 | 108 |
| TF | Factor: E2F-4; motif: GCGGGAAANA | 10318 | 240 |
| TF | Factor: TEL1; motif: CNCGGAANNN | 10420 | 242 |
| TF | Factor: AhR,; motif: NRCGTGNGN | 4421 | 117 |
| TF | Factor: Sp1; motif: NNGGGGCGGGGNN | 8939 | 212 |
| TF | Factor: CACD; motif: CCACRCCC | 10859 | 250 |
| TF | Factor: VDR; motif: GGGKNARNRRGGWSA; match class: 1 | 3798 | 103 |
| TF | Factor: CREB,; motif: NTGACGTNA | 8122 | 195 |
| TF | Factor: USF2; motif: CASGYG | 6304 | 157 |
| TF | Factor: USF2; motif: CASGYG; match class: 1 | 6304 | 157 |
| TF | Factor: Clock; motif: CNGNCACGTGNNNM | 1665 | 53 |
| TF | Factor: AP-2beta; motif: GCNNNGGSCNGVGGGN | 5101 | 131 |
| TF | Factor: Pax-4; motif: NNNNNYCACCCB; match class: 1 | 14458 | 318 |
| TF | Factor: E2F-4; motif: GNNGGCGGGAAN | 5907 | 148 |
| TF | Factor: Zfp281; motif: NNCCCCCCCCCCMYC | 3971 | 106 |
| TF | Factor: WT1; motif: NGCGGGGGGGTSMMCYN | 5297 | 135 |
| TF | Factor: VDR; motif: GGGKNARNRRGGWSA | 10051 | 233 |
| TF | Factor: HNF4alpha1; motif: NRGGNCAAAGGTCAN | 2111 | 63 |
| TF | Factor: C-Myc; motif: NGCCACGTGNN | 6226 | 154 |
| TF | Factor: bach2; motif: TGCTGAGTCAY; match class: 1 | 21 | 4 |
| TF | Factor: ZF5; motif: GSGCGCGR; match class: 1 | 12032 | 271 |
| TF | Factor: E2F-1; motif: GNGGGCGGGRMN; match class: 1 | 10601 | 243 |
| TF | Factor: SREBP-2; motif: NNGYCACNNSMN | 7690 | 184 |
| TF | Factor: Hes1; motif: NNCACGYGNN | 15504 | 336 |
| TF | Factor: Sp1; motif: NGGGGCGGGGN | 9122 | 213 |
| TF | Factor: Egr-1; motif: NNGCGKGGGCGGGG; match class: 1 | 1160 | 39 |
| TF | Factor: LKLF; motif: GGGGTGGKSN | 9186 | 214 |
| TF | Factor: HNF4; motif: TGAMCTTTGNCCN | 2230 | 65 |
| TF | Factor: Mycn; motif: NSCACGTGGC | 154 | 10 |
| TF | Factor: LKLF; motif: CNCCACCCS | 5803 | 144 |
| TF | Factor: Tax/CREB; motif: GGGGGTTGACGYANA | 5338 | 134 |
| TF | Factor: EGR-1; motif: TGCGTGGGCGK | 4136 | 108 |
| TF | Factor: SP2; motif: GNNGGGGGCGGGGSN | 7094 | 171 |
| TF | Factor: CTCF; motif: NAGGGGGCGCNNKNNNN | 14310 | 313 |
| TF | Factor: Tcfl5; motif: NNCNCGNGNN; match class: 1 | 6337 | 155 |
| TF | Factor: Tcfl5; motif: NNCNCGNGNN | 6337 | 155 |
| TF | Factor: GKLF; motif: GCCMCRCCCNNN | 7840 | 186 |
| TF | Factor: Sp5; motif: RNGGRGGNGGRGNNGGGGGAGGRG; match class: 1 | 1948 | 58 |
| TF | Factor: Zic3; motif: NMCCCCCGGGGGGGN; match class: 1 | 2035 | 60 |
| TF | Factor: Sp1; motif: GGNGGGGGNGGGGGMGGGGCNGGG; match class: 1 | 7397 | 177 |
| TF | Factor: E2F; motif: GGCGSG; match class: 1 | 7016 | 169 |
| TF | Factor: Sp5; motif: RNGGRGGNGGRGNNGGGGGAGGRG | 4848 | 123 |
| TF | Factor: Sp1; motif: GGGGCGGGGT | 8345 | 196 |
| TF | Factor: AP-2alphaA; motif: ANNGCCTNAGGSNNT | 5089 | 128 |
| TF | Factor: USF; motif: GYCACGTGNC | 3536 | 94 |
| TF | Factor: CREM; motif: TGACGTCASYN | 5755 | 142 |
| TF | Factor: Kaiso; motif: SARNYCTCGCGAGAN; match class: 1 | 9949 | 228 |
| TF | Factor: CPBP; motif: SNCCCNN; match class: 1 | 19929 | 411 |
| TF | Factor: Sp1; motif: GGGGCGGGGC | 8654 | 202 |
| TF | Factor: c-Myc:Max; motif: GCCAYGYGSN | 7338 | 175 |
| WP | Metapathway biotransformation | 141 | 14 |
| WP | One carbon metabolism and related pathways | 52 | 8 |
| WP | Oxidation by Cytochrome P450 | 40 | 7 |
| WP | Amino Acid metabolism | 95 | 10 |
| WP | Retinol metabolism | 39 | 6 |
2.2.11 Functional Enrichment - Kidney-specific Ahr Regulated
kable(Diff_Kidney_Ahr_PathwayEnrichment$result %>% dplyr::select(source, term_name, term_size, intersection_size),
table.attr = "class=\"striped\"", format = "html")| source | term_name | term_size | intersection_size |
|---|---|---|---|
| CORUM | Parvulin-associated pre-rRNP complex | 46 | 7 |
| GO:BP | small molecule metabolic process | 1713 | 72 |
| GO:BP | organic acid metabolic process | 944 | 44 |
| GO:BP | oxoacid metabolic process | 908 | 42 |
| GO:BP | carboxylic acid metabolic process | 896 | 41 |
| GO:BP | organonitrogen compound biosynthetic process | 1570 | 55 |
| GO:BP | alpha-amino acid metabolic process | 182 | 18 |
| GO:BP | organonitrogen compound metabolic process | 6326 | 130 |
| GO:BP | cellular amide metabolic process | 1077 | 42 |
| GO:BP | metabolic process | 11429 | 193 |
| GO:BP | organic substance catabolic process | 1985 | 59 |
| GO:BP | lipid metabolic process | 1344 | 46 |
| GO:BP | catabolic process | 2399 | 66 |
| GO:BP | cellular amino acid metabolic process | 253 | 19 |
| GO:BP | organic substance metabolic process | 10989 | 186 |
| GO:BP | small molecule catabolic process | 346 | 21 |
| GO:BP | cellular metabolic process | 10350 | 176 |
| GO:BP | small molecule biosynthetic process | 617 | 28 |
| GO:BP | peptide metabolic process | 835 | 32 |
| GO:BP | amide biosynthetic process | 793 | 31 |
| GO:BP | obsolete oxidation-reduction process | 548 | 25 |
| GO:BP | primary metabolic process | 10243 | 172 |
| GO:BP | anion transport | 529 | 24 |
| GO:BP | monocarboxylic acid metabolic process | 616 | 26 |
| GO:BP | sulfur compound metabolic process | 317 | 18 |
| GO:BP | carboxylic acid catabolic process | 221 | 15 |
| GO:BP | organic acid catabolic process | 228 | 15 |
| GO:BP | organic anion transport | 372 | 19 |
| GO:BP | cellular lipid metabolic process | 994 | 33 |
| GO:BP | nucleobase-containing small molecule metabolic process | 537 | 23 |
| GO:BP | cellular catabolic process | 2059 | 52 |
| GO:BP | translation | 657 | 25 |
| GO:BP | organic hydroxy compound metabolic process | 527 | 22 |
| GO:BP | carboxylic acid transport | 297 | 16 |
| GO:BP | peptide biosynthetic process | 677 | 25 |
| GO:BP | nucleotide metabolic process | 466 | 20 |
| GO:BP | fatty acid metabolic process | 425 | 19 |
| GO:BP | nucleoside phosphate metabolic process | 476 | 20 |
| GO:BP | nitrogen compound metabolic process | 9669 | 158 |
| GO:BP | monocarboxylic acid transport | 121 | 10 |
| GO:BP | biosynthetic process | 5882 | 107 |
| GO:BP | alpha-amino acid catabolic process | 80 | 8 |
| GO:BP | alcohol metabolic process | 344 | 16 |
| GO:BP | L-serine biosynthetic process | 4 | 3 |
| GO:BP | alpha-amino acid biosynthetic process | 62 | 7 |
| GO:BP | cellular amino acid biosynthetic process | 62 | 7 |
| GO:BP | organic acid biosynthetic process | 290 | 14 |
| GO:BP | hormone metabolic process | 219 | 12 |
| GO:BP | lipid catabolic process | 335 | 15 |
| GO:BP | organic substance biosynthetic process | 5779 | 103 |
| GO:BP | nucleotide biosynthetic process | 229 | 12 |
| GO:BP | steroid metabolic process | 306 | 14 |
| GO:BP | secondary alcohol biosynthetic process | 50 | 6 |
| GO:BP | cholesterol biosynthetic process | 50 | 6 |
| GO:BP | serine family amino acid biosynthetic process | 16 | 4 |
| GO:BP | nucleoside phosphate biosynthetic process | 232 | 12 |
| GO:BP | cytoplasmic translation | 101 | 8 |
| GO:BP | organonitrogen compound catabolic process | 1249 | 33 |
| GO:BP | organophosphate metabolic process | 891 | 26 |
| GO:BP | purine-containing compound metabolic process | 406 | 16 |
| GO:BP | sulfur compound biosynthetic process | 106 | 8 |
| GO:BP | carboxylic acid biosynthetic process | 282 | 13 |
| GO:BP | sterol biosynthetic process | 56 | 6 |
| GO:BP | secondary alcohol metabolic process | 141 | 9 |
| GO:BP | cellular biosynthetic process | 5715 | 100 |
| GO:BP | serine family amino acid metabolic process | 37 | 5 |
| GO:BP | acetyl-CoA metabolic process | 37 | 5 |
| GO:BP | L-serine metabolic process | 8 | 3 |
| GO:BP | regulation of biological quality | 3876 | 73 |
| GO:BP | amine metabolic process | 119 | 8 |
| GO:BP | monocarboxylic acid catabolic process | 122 | 8 |
| GO:BP | cellular amino acid catabolic process | 92 | 7 |
| GO:BP | lipid transport | 401 | 15 |
| GO:BP | cellular nitrogen compound metabolic process | 6201 | 105 |
| GO:BP | aspartate family amino acid metabolic process | 43 | 5 |
| GO:BP | steroid biosynthetic process | 161 | 9 |
| GO:BP | cholesterol metabolic process | 129 | 8 |
| GO:BP | negative regulation of ubiquitin protein ligase activity | 11 | 3 |
| GO:BP | cellular hormone metabolic process | 135 | 8 |
| GO:BP | alcohol biosynthetic process | 136 | 8 |
| GO:BP | sterol metabolic process | 137 | 8 |
| GO:BP | negative regulation of ERBB signaling pathway | 27 | 4 |
| GO:BP | purine nucleotide metabolic process | 385 | 14 |
| GO:BP | astral microtubule organization | 12 | 3 |
| GO:BP | cellular modified amino acid metabolic process | 179 | 9 |
| GO:BP | cellular amine metabolic process | 110 | 7 |
| GO:BP | L-alanine import across plasma membrane | 3 | 2 |
| GO:BP | purine nucleoside bisphosphate metabolic process | 110 | 7 |
| GO:BP | ribonucleoside bisphosphate metabolic process | 110 | 7 |
| GO:BP | nucleoside bisphosphate metabolic process | 110 | 7 |
| GO:BP | short-chain fatty acid metabolic process | 13 | 3 |
| GO:BP | tryptophan metabolic process | 13 | 3 |
| GO:BP | indolalkylamine metabolic process | 13 | 3 |
| GO:BP | lipid biosynthetic process | 647 | 19 |
| GO:BP | carbohydrate derivative metabolic process | 975 | 25 |
| GO:BP | fatty acid oxidation | 114 | 7 |
| GO:BP | organophosphate biosynthetic process | 500 | 16 |
| GO:BP | organic cyclic compound catabolic process | 458 | 15 |
| GO:BP | terpenoid metabolic process | 85 | 6 |
| GO:BP | lipid localization | 459 | 15 |
| GO:BP | cellular nitrogen compound catabolic process | 411 | 14 |
| GO:BP | sulfur amino acid metabolic process | 33 | 4 |
| GO:BP | lipid oxidation | 120 | 7 |
| GO:BP | gap junction assembly | 16 | 3 |
| GO:BP | glycine metabolic process | 16 | 3 |
| GO:BP | N-glycan processing | 16 | 3 |
| GO:BP | cytoplasmic translational initiation | 35 | 4 |
| GO:BP | kidney development | 327 | 12 |
| GO:BP | formation of cytoplasmic translation initiation complex | 16 | 3 |
| GO:BP | ribonucleotide metabolic process | 376 | 13 |
| GO:BP | NAD biosynthetic process | 16 | 3 |
| GO:BP | primary alcohol metabolic process | 90 | 6 |
| GO:BP | L-alanine transmembrane transport | 4 | 2 |
| GO:BP | acyl-CoA metabolic process | 94 | 6 |
| GO:BP | renal system development | 338 | 12 |
| GO:BP | sodium-independent organic anion transport | 17 | 3 |
| GO:BP | thioester metabolic process | 94 | 6 |
| GO:BP | ribose phosphate metabolic process | 385 | 13 |
| GO:BP | ion transport | 1572 | 34 |
| GO:BP | oligosaccharide metabolic process | 38 | 4 |
| GO:BP | cellular biogenic amine metabolic process | 97 | 6 |
| GO:BP | negative regulation of ubiquitin-protein transferase activity | 18 | 3 |
| GO:BP | inorganic anion transport | 171 | 8 |
| GO:BP | triglyceride transport | 5 | 2 |
| GO:BP | negative regulation of protein neddylation | 5 | 2 |
| GO:BP | acylglycerol transport | 5 | 2 |
| GO:BP | cellular ketone metabolic process | 213 | 9 |
| GO:BP | fatty acid catabolic process | 99 | 6 |
| GO:BP | cellular lipid catabolic process | 214 | 9 |
| GO:BP | deoxyribonucleoside monophosphate catabolic process | 19 | 3 |
| GO:BP | purine nucleobase metabolic process | 19 | 3 |
| GO:BP | acetyl-CoA biosynthetic process | 19 | 3 |
| GO:CC | cytoplasm | 11093 | 199 |
| GO:CC | cytosolic ribosome | 112 | 14 |
| GO:CC | cytosolic small ribosomal subunit | 45 | 9 |
| GO:CC | intracellular anatomical structure | 14111 | 213 |
| GO:CC | ribosomal subunit | 200 | 15 |
| GO:CC | small ribosomal subunit | 79 | 10 |
| GO:CC | cytosol | 3849 | 83 |
| GO:CC | ribosome | 236 | 15 |
| GO:CC | brush border | 134 | 11 |
| GO:CC | cluster of actin-based cell projections | 193 | 12 |
| GO:CC | intracellular organelle | 12510 | 186 |
| GO:CC | cellular anatomical entity | 19567 | 254 |
| GO:CC | organelle | 12827 | 189 |
| GO:CC | ribonucleoprotein complex | 725 | 23 |
| GO:CC | brush border membrane | 73 | 7 |
| GO:CC | intracellular membrane-bounded organelle | 11363 | 170 |
| GO:CC | membrane-bounded organelle | 11812 | 175 |
| GO:CC | endoplasmic reticulum | 1761 | 40 |
| GO:CC | eukaryotic translation initiation factor 3 complex, eIF3e | 2 | 2 |
| GO:CC | mitochondrion | 1827 | 40 |
| GO:CC | endomembrane system | 4006 | 72 |
| GO:CC | eukaryotic translation elongation factor 1 complex | 3 | 2 |
| GO:CC | organelle envelope | 1176 | 28 |
| GO:CC | envelope | 1176 | 28 |
| GO:CC | mitochondrial matrix | 341 | 12 |
| GO:CC | cytosolic large ribosomal subunit | 64 | 5 |
| GO:CC | intracellular non-membrane-bounded organelle | 4500 | 76 |
| GO:CC | non-membrane-bounded organelle | 4515 | 76 |
| GO:CC | nuclear envelope | 460 | 14 |
| GO:CC | polysome | 70 | 5 |
| GO:CC | organelle membrane | 3076 | 55 |
| GO:CC | collagen network | 7 | 2 |
| GO:CC | collagen type IV trimer | 7 | 2 |
| GO:CC | basement membrane collagen trimer | 7 | 2 |
| GO:CC | network-forming collagen trimer | 7 | 2 |
| GO:MF | catalytic activity | 5665 | 121 |
| GO:MF | structural constituent of ribosome | 172 | 14 |
| GO:MF | rRNA binding | 69 | 9 |
| GO:MF | 5S rRNA binding | 13 | 5 |
| GO:MF | oxidoreductase activity | 815 | 29 |
| GO:MF | identical protein binding | 2140 | 49 |
| GO:MF | flavin adenine dinucleotide binding | 90 | 8 |
| GO:MF | transporter activity | 1137 | 32 |
| GO:MF | RNA binding | 1267 | 34 |
| GO:MF | organic acid transmembrane transporter activity | 156 | 10 |
| GO:MF | dipeptidase activity | 15 | 4 |
| GO:MF | carboxylic acid transmembrane transporter activity | 155 | 10 |
| GO:MF | secondary active transmembrane transporter activity | 232 | 12 |
| GO:MF | transmembrane transporter activity | 1053 | 29 |
| GO:MF | amide binding | 367 | 15 |
| GO:MF | monocarboxylic acid transmembrane transporter activity | 56 | 6 |
| GO:MF | structural molecule activity | 612 | 20 |
| GO:MF | anion transmembrane transporter activity | 295 | 13 |
| GO:MF | metallodipeptidase activity | 8 | 3 |
| GO:MF | asparaginase activity | 2 | 2 |
| GO:MF | single-stranded RNA binding | 92 | 7 |
| GO:MF | ubiquitin ligase inhibitor activity | 9 | 3 |
| GO:MF | lyase activity | 198 | 10 |
| GO:MF | ubiquitin-protein transferase inhibitor activity | 10 | 3 |
| GO:MF | mRNA 5’-UTR binding | 25 | 4 |
| GO:MF | vitamin binding | 141 | 8 |
| GO:MF | inorganic anion transmembrane transporter activity | 142 | 8 |
| GO:MF | active transmembrane transporter activity | 346 | 13 |
| GO:MF | D5 dopamine receptor binding | 3 | 2 |
| GO:MF | oleic acid binding | 3 | 2 |
| GO:MF | translation regulator activity | 145 | 8 |
| GO:MF | translation regulator activity, nucleic acid binding | 113 | 7 |
| GO:MF | carbon-carbon lyase activity | 55 | 5 |
| GO:MF | small molecule binding | 2543 | 50 |
| GO:MF | binding | 14895 | 208 |
| GO:MF | sodium-independent organic anion transmembrane transporter activity | 16 | 3 |
| GO:MF | intramolecular oxidoreductase activity, transposing C=C bonds | 17 | 3 |
| GO:MF | exopeptidase activity | 96 | 6 |
| GO:MF | translation factor activity, RNA binding | 96 | 6 |
| GO:MF | transferase activity, transferring alkyl or aryl (other than methyl) groups | 65 | 5 |
| GO:MF | mRNA binding | 394 | 13 |
| GO:MF | actin binding | 443 | 14 |
| GO:MF | AMP binding | 18 | 3 |
| GO:MF | organic anion transmembrane transporter activity | 172 | 8 |
| GO:MF | protein binding | 10189 | 151 |
| GO:MF | long-chain-acyl-CoA dehydrogenase activity | 5 | 2 |
| GO:MF | carboxypeptidase activity | 41 | 4 |
| GO:MF | sialyltransferase activity | 20 | 3 |
| GO:MF | lysophospholipase activity | 20 | 3 |
| GO:MF | acetyl-CoA C-acetyltransferase activity | 6 | 2 |
| GO:MF | anion binding | 2420 | 46 |
| GO:MF | hydrolase activity | 2353 | 45 |
| GO:MF | alpha-N-acetylneuraminate alpha-2,8-sialyltransferase activity | 6 | 2 |
| GO:MF | hydrolase activity, acting on ester bonds | 735 | 19 |
| GO:MF | steroid delta-isomerase activity | 6 | 2 |
| GO:MF | lipid transporter activity | 147 | 7 |
| GO:MF | ubiquitin-protein transferase regulator activity | 22 | 3 |
| GO:MF | hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides | 77 | 5 |
| GO:MF | anion:anion antiporter activity | 23 | 3 |
| GO:MF | thyroid hormone binding | 7 | 2 |
| GO:MF | carboxylic ester hydrolase activity | 153 | 7 |
| GO:MF | dopamine receptor binding | 24 | 3 |
| HP | Elevated red cell adenosine deaminase level | 18 | 5 |
| HP | Abnormal radial artery morphology | 18 | 5 |
| HP | Macrocytic anemia | 58 | 8 |
| HP | Macrocytic dyserythropoietic anemia | 19 | 5 |
| HP | Thrombocytosis | 46 | 7 |
| HP | Radial artery aplasia | 18 | 5 |
| HP | Erythroid hypoplasia | 21 | 5 |
| HP | Increased mean corpuscular volume | 35 | 6 |
| HP | Malignant genitourinary tract tumor | 22 | 5 |
| HP | Pure red cell aplasia | 23 | 5 |
| HP | Adenocarcinoma of the colon | 23 | 5 |
| HP | Nonimmune hydrops fetalis | 38 | 6 |
| HP | Abnormal circulating serine concentration | 5 | 3 |
| HP | Persistence of hemoglobin F | 25 | 5 |
| HP | Abnormality of the thenar eminence | 25 | 5 |
| HP | Abnormal erythrocyte enzyme level | 26 | 5 |
| HP | Adenocarcinoma of the large intestine | 26 | 5 |
| HP | Osteosarcoma | 28 | 5 |
| HP | Abnormal mean corpuscular volume | 45 | 6 |
| HP | Normochromic anemia | 29 | 5 |
| HP | Reticulocytopenia | 29 | 5 |
| HP | Increased lactate dehydrogenase level | 31 | 5 |
| HP | Adenocarcinoma of the intestines | 31 | 5 |
| HP | Duplication of thumb phalanx | 49 | 6 |
| HP | Elevated 8(9)-cholestenol | 2 | 2 |
| HP | Hypoglycinemia | 2 | 2 |
| HP | Abnormal number of erythroid precursors | 34 | 5 |
| HP | Partial duplication of thumb phalanx | 33 | 5 |
| HP | Elevated 8-dehydrocholesterol | 2 | 2 |
| HP | Systemic lupus erythematosus | 34 | 5 |
| HP | Partial duplication of the phalanx of hand | 35 | 5 |
| HP | Abnormal platelet count | 351 | 16 |
| HP | Antinuclear antibody positivity | 37 | 5 |
| HP | Horseshoe kidney | 80 | 7 |
| HP | Cleft soft palate | 160 | 10 |
| HP | Gastrointestinal carcinoma | 64 | 6 |
| HP | EEG with central epileptiform discharges | 3 | 2 |
| HP | Bilateral perisylvian polymicrogyria | 3 | 2 |
| HP | Nephritis | 60 | 6 |
| HP | Thrombocytopenia | 333 | 15 |
| HP | Body odor | 3 | 2 |
| HP | Glomerular basement membrane lamellation | 3 | 2 |
| HP | Malar rash | 11 | 3 |
| HP | Absent thumb | 43 | 5 |
| HP | Acute myeloid leukemia | 63 | 6 |
| HP | Perisylvian predominant thick cortex pachygyria | 3 | 2 |
| HP | Thin glomerular basement membrane | 3 | 2 |
| HP | Oral aversion | 3 | 2 |
| HP | Abnormal enzyme/coenzyme activity | 477 | 19 |
| HP | Hyposerinemia | 3 | 2 |
| HP | Malignant gastrointestinal tract tumors | 64 | 6 |
| HP | EEG with parietal focal spikes | 3 | 2 |
| HP | EEG with central focal spikes | 3 | 2 |
| HP | Abnormal reticulocyte morphology | 64 | 6 |
| HP | Neoplasm of the gastrointestinal tract | 261 | 13 |
| KEGG | Metabolic pathways | 1563 | 58 |
| KEGG | Ribosome | 169 | 14 |
| KEGG | Coronavirus disease - COVID-19 | 241 | 16 |
| KEGG | Steroid biosynthesis | 20 | 5 |
| KEGG | Glycine, serine and threonine metabolism | 39 | 6 |
| KEGG | Glyoxylate and dicarboxylate metabolism | 31 | 5 |
| KEGG | Glutathione metabolism | 71 | 6 |
| REAC | GTP hydrolysis and joining of the 60S ribosomal subunit | 109 | 18 |
| REAC | L13a-mediated translational silencing of Ceruloplasmin expression | 108 | 18 |
| REAC | Cap-dependent Translation Initiation | 116 | 18 |
| REAC | Eukaryotic Translation Initiation | 116 | 18 |
| REAC | Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S | 57 | 13 |
| REAC | Formation of a pool of free 40S subunits | 98 | 16 |
| REAC | Ribosomal scanning and start codon recognition | 56 | 13 |
| REAC | Translation initiation complex formation | 56 | 13 |
| REAC | Formation of the ternary complex, and subsequently, the 43S complex | 49 | 12 |
| REAC | SRP-dependent cotranslational protein targeting to membrane | 89 | 14 |
| REAC | Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) | 91 | 14 |
| REAC | Translation | 217 | 20 |
| REAC | Nonsense-Mediated Decay (NMD) | 110 | 14 |
| REAC | Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) | 110 | 14 |
| REAC | Metabolism | 1679 | 60 |
| REAC | Major pathway of rRNA processing in the nucleolus and cytosol | 167 | 15 |
| REAC | rRNA processing | 167 | 15 |
| REAC | rRNA processing in the nucleus and cytosol | 167 | 15 |
| REAC | Sialic acid metabolism | 30 | 6 |
| REAC | Metabolism of amino acids and derivatives | 234 | 15 |
| REAC | Synthesis of substrates in N-glycan biosythesis | 58 | 6 |
| REAC | SLC-mediated transmembrane transport | 218 | 12 |
| REAC | Metabolism of RNA | 532 | 21 |
| REAC | Cholesterol biosynthesis | 25 | 4 |
| REAC | ARL13B-mediated ciliary trafficking of INPP5E | 3 | 2 |
| REAC | Metabolism of nucleotides | 91 | 7 |
| REAC | Biosynthesis of the N-glycan precursor (dolichol lipid-linked oligosaccharide, LLO) and transfer to a nascent protein | 68 | 6 |
| REAC | Cholesterol biosynthesis via desmosterol | 4 | 2 |
| REAC | Transport of inorganic cations/anions and amino acids/oligopeptides | 96 | 7 |
| REAC | Cholesterol biosynthesis via lathosterol | 4 | 2 |
| TF | Factor: E2F-1; motif: GNGGGCGGGRMN | 14228 | 213 |
| TF | Factor: BEN; motif: CAGCGRNV | 16234 | 231 |
| TF | Factor: USF2; motif: NNNCCACGTGACN | 3892 | 76 |
| TF | Factor: FOXN4; motif: NNWANNCGWMCGCGTCNNNNMT | 16009 | 226 |
| TF | Factor: Hes1; motif: NNCACGYGNN; match class: 1 | 11386 | 172 |
| WP | Cytoplasmic Ribosomal Proteins | 81 | 12 |
| WP | mRNA processing | 444 | 22 |
| WP | Translation Factors | 49 | 6 |
| WP | One carbon metabolism and related pathways | 52 | 6 |
| WP | Cholesterol metabolism (includes both Bloch and Kandutsch-Russell pathways) | 51 | 6 |
2.2.12 Functional Enrichment - Liver and Kidney TCDD-AhR Regulated
kable(TissueIntersect_Interx_PathwayEnrichment$result %>% dplyr::select(source, term_name, term_size, intersection_size),
table.attr = "class=\"striped\"", format = "html")| source | term_name | term_size | intersection_size |
|---|---|---|---|
| GO:BP | estrogen metabolic process | 27 | 2 |
| GO:BP | cellular hormone metabolic process | 135 | 2 |
| GO:BP | dibenzo-p-dioxin catabolic process | 1 | 1 |
| GO:BP | hormone metabolic process | 219 | 2 |
| GO:BP | insecticide metabolic process | 2 | 1 |
| GO:BP | phenylpropanoid metabolic process | 6 | 1 |
| GO:BP | response to nematode | 5 | 1 |
| GO:BP | coumarin metabolic process | 6 | 1 |
| GO:BP | dibenzo-p-dioxin metabolic process | 4 | 1 |
| GO:BP | response to iron(III) ion | 6 | 1 |
| GO:BP | response to 2,3,7,8-tetrachlorodibenzodioxine | 4 | 1 |
| GO:BP | lipid hydroxylation | 3 | 1 |
| GO:BP | steroid metabolic process | 306 | 2 |
| GO:BP | 9-cis-retinoic acid biosynthetic process | 7 | 1 |
| GO:BP | 9-cis-retinoic acid metabolic process | 7 | 1 |
| GO:BP | positive regulation of neurotrophin TRK receptor signaling pathway | 8 | 1 |
| GO:BP | response to herbicide | 8 | 1 |
| GO:BP | response to insecticide | 13 | 1 |
| GO:BP | parturition | 14 | 1 |
| GO:BP | xenobiotic catabolic process | 15 | 1 |
| GO:BP | cellular response to organic cyclic compound | 595 | 2 |
| GO:BP | terpenoid biosynthetic process | 17 | 1 |
| GO:BP | diterpenoid biosynthetic process | 11 | 1 |
| GO:BP | regulation of hormone levels | 559 | 2 |
| GO:BP | protein mono-ADP-ribosylation | 11 | 1 |
| GO:BP | activation of cysteine-type endopeptidase activity | 14 | 1 |
| GO:BP | retinoic acid biosynthetic process | 11 | 1 |
| GO:BP | flavonoid metabolic process | 14 | 1 |
| GO:BP | transmembrane receptor protein tyrosine kinase signaling pathway | 587 | 2 |
| GO:BP | toxin metabolic process | 17 | 1 |
| GO:BP | regulation of neurotrophin TRK receptor signaling pathway | 16 | 1 |
| GO:BP | maternal process involved in parturition | 9 | 1 |
| GO:BP | cellular response to organic substance | 2453 | 3 |
| GO:BP | protein auto-ADP-ribosylation | 12 | 1 |
| GO:BP | hydrogen peroxide biosynthetic process | 18 | 1 |
| GO:BP | hepatocyte differentiation | 19 | 1 |
| GO:BP | cellular response to copper ion | 20 | 1 |
| GO:BP | response to vitamin A | 22 | 1 |
| GO:BP | cellular response to chemical stimulus | 3097 | 3 |
| GO:BP | androgen metabolic process | 24 | 1 |
| GO:BP | response to hyperoxia | 25 | 1 |
| GO:BP | retinoic acid metabolic process | 27 | 1 |
| GO:BP | smooth muscle tissue development | 28 | 1 |
| GO:BP | response to iron ion | 36 | 1 |
| GO:BP | response to immobilization stress | 33 | 1 |
| GO:BP | face morphogenesis | 34 | 1 |
| GO:BP | positive regulation of G1/S transition of mitotic cell cycle | 36 | 1 |
| GO:BP | isoprenoid biosynthetic process | 33 | 1 |
| GO:BP | neurotrophin TRK receptor signaling pathway | 31 | 1 |
| GO:BP | response to copper ion | 33 | 1 |
| GO:BP | response to arsenic-containing substance | 35 | 1 |
| GO:BP | response to organic substance | 3418 | 3 |
| GO:BP | response to increased oxygen levels | 32 | 1 |
| GO:BP | protein ADP-ribosylation | 35 | 1 |
| GO:BP | porphyrin-containing compound metabolic process | 37 | 1 |
| GO:BP | enzyme linked receptor protein signaling pathway | 916 | 2 |
| GO:BP | head morphogenesis | 40 | 1 |
| GO:BP | dendrite extension | 43 | 1 |
| GO:BP | neurotrophin signaling pathway | 43 | 1 |
| GO:BP | regulation of biological quality | 3876 | 3 |
| GO:BP | response to food | 45 | 1 |
| GO:BP | tetrapyrrole metabolic process | 46 | 1 |
| GO:BP | retinol metabolic process | 47 | 1 |
| GO:BP | positive regulation of cell cycle G1/S phase transition | 48 | 1 |
| GO:BP | response to organic cyclic compound | 1043 | 2 |
| GO:BP | hydrogen peroxide metabolic process | 51 | 1 |
| GO:BP | face development | 52 | 1 |
| GO:BP | body morphogenesis | 54 | 1 |
| GO:BP | reactive oxygen species biosynthetic process | 56 | 1 |
| GO:BP | tube development | 1137 | 2 |
| GO:BP | response to antibiotic | 59 | 1 |
| GO:BP | platelet-derived growth factor receptor signaling pathway | 60 | 1 |
| GO:BP | secondary metabolic process | 61 | 1 |
| GO:BP | DNA methylation | 64 | 1 |
| GO:BP | DNA alkylation | 64 | 1 |
| GO:BP | cell differentiation | 4378 | 3 |
| GO:BP | cellular developmental process | 4454 | 3 |
| GO:BP | zymogen activation | 66 | 1 |
| GO:BP | demethylation | 68 | 1 |
| GO:BP | drug metabolic process | 68 | 1 |
| GO:BP | retinoid metabolic process | 71 | 1 |
| GO:BP | diterpenoid metabolic process | 77 | 1 |
| GO:MF | flavonoid 3’-monooxygenase activity | 1 | 1 |
| GO:MF | estrogen 2-hydroxylase activity | 3 | 1 |
| GO:MF | vitamin D 24-hydroxylase activity | 2 | 1 |
| GO:MF | oxidoreductase activity, acting on diphenols and related substances as donors | 7 | 1 |
| GO:MF | hydroperoxy icosatetraenoate dehydratase activity | 7 | 1 |
| GO:MF | estrogen 16-alpha-hydroxylase activity | 12 | 1 |
| GO:MF | protein ADP-ribosylase activity | 15 | 1 |
| GO:MF | NAD+ ADP-ribosyltransferase activity | 23 | 1 |
| GO:MF | aromatase activity | 36 | 1 |
| GO:MF | demethylase activity | 40 | 1 |
| GO:MF | oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen | 54 | 1 |
| GO:MF | Hsp90 protein binding | 45 | 1 |
| GO:MF | arachidonic acid monooxygenase activity | 42 | 1 |
| GO:MF | Hsp70 protein binding | 51 | 1 |
| GO:MF | pentosyltransferase activity | 52 | 1 |
| GO:MF | hydro-lyase activity | 61 | 1 |
| GO:MF | oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen | 65 | 1 |
| GO:MF | steroid hydroxylase activity | 69 | 1 |
| GO:MF | carbon-oxygen lyase activity | 78 | 1 |
| KEGG | Chemical carcinogenesis | 101 | 1 |
| KEGG | Ovarian steroidogenesis | 62 | 1 |
| KEGG | Metabolism of xenobiotics by cytochrome P450 | 73 | 1 |
| KEGG | Retinol metabolism | 97 | 1 |
| KEGG | Tryptophan metabolism | 51 | 1 |
| KEGG | Steroid hormone biosynthesis | 91 | 1 |
| REAC | Synthesis of epoxy (EET) and dihydroxyeicosatrienoic acids (DHET) | 7 | 1 |
| REAC | Synthesis of (16-20)-hydroxyeicosatetraenoic acids (HETE) | 8 | 1 |
| REAC | Biosynthesis of protectins | 3 | 1 |
| REAC | Biosynthesis of specialized proresolving mediators (SPMs) | 17 | 1 |
| REAC | Biosynthesis of DHA-derived SPMs | 16 | 1 |
| REAC | Xenobiotics | 25 | 1 |
| REAC | RHO GTPases Activate WASPs and WAVEs | 33 | 1 |
| REAC | Arachidonic acid metabolism | 61 | 1 |
| REAC | Cytochrome P450 - arranged by substrate type | 71 | 1 |
| WP | Fatty Acid Omega Oxidation | 7 | 1 |
| WP | Estrogen metabolism | 14 | 1 |
| WP | Oxidative Stress | 28 | 1 |
| WP | Oxidation by Cytochrome P450 | 40 | 1 |
| WP | Tryptophan metabolism | 44 | 1 |
2.2.13 Functional Enrichment - Liver-specific TCDD-AhR Regulated
kable(Diff_Liver_Interx_PathwayEnrichment$result %>% dplyr::select(source, term_name, term_size, intersection_size),
table.attr = "class=\"striped\"", format = "html")| source | term_name | term_size | intersection_size |
|---|---|---|---|
| CORUM | Parvulin-associated pre-rRNP complex | 46 | 9 |
| GO:BP | cellular amide metabolic process | 1077 | 55 |
| GO:BP | organonitrogen compound biosynthetic process | 1570 | 65 |
| GO:BP | cellular metabolic process | 10350 | 212 |
| GO:BP | small molecule metabolic process | 1713 | 68 |
| GO:BP | organic acid metabolic process | 944 | 48 |
| GO:BP | peptide metabolic process | 835 | 45 |
| GO:BP | metabolic process | 11429 | 224 |
| GO:BP | carboxylic acid metabolic process | 896 | 45 |
| GO:BP | oxoacid metabolic process | 908 | 45 |
| GO:BP | obsolete oxidation-reduction process | 548 | 34 |
| GO:BP | peptide biosynthetic process | 677 | 37 |
| GO:BP | organic substance metabolic process | 10989 | 212 |
| GO:BP | amide biosynthetic process | 793 | 40 |
| GO:BP | translation | 657 | 36 |
| GO:BP | monocarboxylic acid metabolic process | 616 | 34 |
| GO:BP | organic acid biosynthetic process | 290 | 23 |
| GO:BP | catabolic process | 2399 | 74 |
| GO:BP | primary metabolic process | 10243 | 198 |
| GO:BP | organonitrogen compound metabolic process | 6326 | 140 |
| GO:BP | organic substance catabolic process | 1985 | 63 |
| GO:BP | carboxylic acid biosynthetic process | 282 | 21 |
| GO:BP | cellular lipid metabolic process | 994 | 41 |
| GO:BP | cellular catabolic process | 2059 | 64 |
| GO:BP | small molecule biosynthetic process | 617 | 31 |
| GO:BP | sulfur compound metabolic process | 317 | 21 |
| GO:BP | lipid metabolic process | 1344 | 47 |
| GO:BP | ribonucleoprotein complex biogenesis | 413 | 23 |
| GO:BP | fatty acid metabolic process | 425 | 23 |
| GO:BP | regulation of biological quality | 3876 | 92 |
| GO:BP | biosynthetic process | 5882 | 124 |
| GO:BP | cytoplasmic translation | 101 | 11 |
| GO:BP | ribosome assembly | 63 | 9 |
| GO:BP | organic substance biosynthetic process | 5779 | 120 |
| GO:BP | ribosome biogenesis | 288 | 17 |
| GO:BP | ribonucleoprotein complex assembly | 182 | 13 |
| GO:BP | small molecule catabolic process | 346 | 18 |
| GO:BP | ribonucleoprotein complex subunit organization | 188 | 13 |
| GO:BP | cellular biosynthetic process | 5715 | 116 |
| GO:BP | nitrogen compound metabolic process | 9669 | 174 |
| GO:BP | benzene-containing compound metabolic process | 30 | 6 |
| GO:BP | monocarboxylic acid biosynthetic process | 194 | 13 |
| GO:BP | glutathione metabolic process | 70 | 8 |
| GO:BP | cellular modified amino acid metabolic process | 179 | 12 |
| GO:BP | organophosphate metabolic process | 891 | 30 |
| GO:BP | fatty acid biosynthetic process | 151 | 11 |
| GO:BP | NADP metabolic process | 38 | 6 |
| GO:BP | unsaturated fatty acid metabolic process | 133 | 10 |
| GO:BP | glycosyl compound metabolic process | 86 | 8 |
| GO:BP | response to hormone | 912 | 29 |
| GO:BP | response to toxic substance | 240 | 13 |
| GO:BP | rRNA processing | 208 | 12 |
| GO:BP | gland development | 513 | 20 |
| GO:BP | cell redox homeostasis | 29 | 5 |
| GO:BP | cellular lipid catabolic process | 214 | 12 |
| GO:BP | ribosomal small subunit biogenesis | 69 | 7 |
| GO:BP | protein metabolic process | 5474 | 107 |
| GO:BP | mature ribosome assembly | 6 | 3 |
| GO:BP | rRNA metabolic process | 217 | 12 |
| GO:BP | carboxylic acid catabolic process | 221 | 12 |
| GO:BP | organonitrogen compound catabolic process | 1249 | 35 |
| GO:BP | toxin metabolic process | 17 | 4 |
| GO:BP | carbohydrate metabolic process | 587 | 21 |
| GO:BP | very long-chain fatty acid metabolic process | 33 | 5 |
| GO:BP | monoacylglycerol catabolic process | 7 | 3 |
| GO:BP | organic acid catabolic process | 228 | 12 |
| GO:BP | ketone catabolic process | 18 | 4 |
| GO:BP | positive regulation of cellular amide metabolic process | 163 | 10 |
| GO:BP | nucleobase metabolic process | 34 | 5 |
| GO:BP | regulation of angiogenesis | 305 | 14 |
| GO:BP | homeostatic process | 1922 | 47 |
| GO:BP | carbohydrate derivative metabolic process | 975 | 29 |
| GO:BP | purine nucleobase metabolic process | 19 | 4 |
| GO:BP | positive regulation of translation | 135 | 9 |
| GO:BP | cellular protein metabolic process | 4815 | 95 |
| GO:BP | blood vessel morphogenesis | 647 | 22 |
| GO:BP | regulation of vasculature development | 310 | 14 |
| GO:BP | alpha-amino acid catabolic process | 80 | 7 |
| GO:BP | cellular detoxification | 108 | 8 |
| GO:BP | cellular nitrogen compound metabolic process | 6201 | 116 |
| GO:BP | androgen biosynthetic process | 8 | 3 |
| GO:BP | ribosomal small subunit assembly | 20 | 4 |
| GO:BP | regulation of cellular amide metabolic process | 438 | 17 |
| GO:BP | liver development | 173 | 10 |
| GO:BP | cellular aldehyde metabolic process | 59 | 6 |
| GO:BP | hepaticobiliary system development | 176 | 10 |
| GO:BP | response to insulin | 284 | 13 |
| GO:BP | cellular response to toxic substance | 115 | 8 |
| GO:BP | long-chain fatty acid metabolic process | 115 | 8 |
| GO:BP | NADPH oxidation | 9 | 3 |
| GO:BP | cellular process | 17828 | 270 |
| GO:BP | response to xenobiotic stimulus | 115 | 8 |
| GO:BP | nucleoside metabolic process | 61 | 6 |
| GO:BP | nucleobase-containing small molecule metabolic process | 537 | 19 |
| GO:BP | response to oxygen radical | 22 | 4 |
| GO:BP | response to superoxide | 22 | 4 |
| GO:BP | response to oxygen-containing compound | 1820 | 44 |
| GO:BP | cellular response to chemical stimulus | 3097 | 66 |
| GO:BP | angiogenesis | 545 | 19 |
| GO:BP | localization | 6168 | 114 |
| GO:BP | liver regeneration | 42 | 5 |
| GO:BP | lipid catabolic process | 335 | 14 |
| GO:BP | animal organ regeneration | 91 | 7 |
| GO:BP | regulation of translation | 377 | 15 |
| GO:BP | positive regulation of establishment of protein localization to telomere | 10 | 3 |
| GO:BP | negative regulation of cell adhesion mediated by integrin | 10 | 3 |
| GO:BP | cellular amino acid catabolic process | 92 | 7 |
| GO:BP | membrane lipid metabolic process | 187 | 10 |
| GO:BP | androgen metabolic process | 24 | 4 |
| GO:BP | lipid biosynthetic process | 647 | 21 |
| GO:BP | blood vessel development | 743 | 23 |
| GO:BP | detoxification | 123 | 8 |
| GO:BP | ribosomal large subunit biogenesis | 69 | 6 |
| GO:BP | regulation of establishment of protein localization to telomere | 11 | 3 |
| GO:BP | kynurenine metabolic process | 11 | 3 |
| GO:BP | anatomical structure formation involved in morphogenesis | 1165 | 31 |
| GO:BP | tube morphogenesis | 911 | 26 |
| GO:BP | maturation of LSU-rRNA | 27 | 4 |
| GO:BP | lactation | 72 | 6 |
| GO:BP | regulation of establishment of protein localization to chromosome | 12 | 3 |
| GO:BP | xenobiotic metabolic process | 102 | 7 |
| GO:BP | vasculature development | 773 | 23 |
| GO:BP | regulation of endocannabinoid signaling pathway | 3 | 2 |
| GO:BP | response to oxidative stress | 447 | 16 |
| GO:BP | positive regulation of DNA biosynthetic process | 74 | 6 |
| GO:BP | icosanoid metabolic process | 134 | 8 |
| GO:BP | ncRNA processing | 363 | 14 |
| GO:BP | response to peptide hormone | 452 | 16 |
| GO:BP | mammary gland development | 170 | 9 |
| GO:BP | monoacylglycerol metabolic process | 13 | 3 |
| GO:BP | positive regulation of protein localization to chromosome, telomeric region | 13 | 3 |
| GO:BP | cellular response to xenobiotic stimulus | 106 | 7 |
| GO:BP | response to drug | 459 | 16 |
| GO:BP | prostanoid metabolic process | 52 | 5 |
| GO:BP | prostaglandin metabolic process | 52 | 5 |
| GO:BP | sphingolipid metabolic process | 140 | 8 |
| GO:BP | cellular ketone metabolic process | 213 | 10 |
| GO:BP | aldehyde catabolic process | 14 | 3 |
| GO:BP | cellular amino acid metabolic process | 253 | 11 |
| GO:BP | protein localization to organelle | 859 | 24 |
| GO:BP | regulation of complement activation | 15 | 3 |
| GO:BP | establishment of localization | 4658 | 88 |
| GO:BP | xenobiotic catabolic process | 15 | 3 |
| GO:BP | alpha-amino acid metabolic process | 182 | 9 |
| GO:BP | regulation of protein localization to chromosome, telomeric region | 15 | 3 |
| GO:BP | negative regulation of osteoblast differentiation | 56 | 5 |
| GO:BP | nitrobenzene metabolic process | 4 | 2 |
| GO:BP | glutathione derivative metabolic process | 4 | 2 |
| GO:BP | negative regulation of endothelial cell chemotaxis | 4 | 2 |
| GO:BP | L-kynurenine catabolic process | 4 | 2 |
| GO:BP | cell death | 2136 | 47 |
| GO:BP | glutathione derivative biosynthetic process | 4 | 2 |
| GO:BP | cellular response to insulin stimulus | 222 | 10 |
| GO:BP | establishment of protein localization to telomere | 16 | 3 |
| GO:BP | nucleobase biosynthetic process | 16 | 3 |
| GO:BP | response to organic substance | 3418 | 68 |
| GO:BP | aromatic amino acid family catabolic process | 16 | 3 |
| GO:BP | ribosomal subunit export from nucleus | 16 | 3 |
| GO:BP | ribosome localization | 16 | 3 |
| GO:BP | formation of cytoplasmic translation initiation complex | 16 | 3 |
| GO:BP | tube development | 1137 | 29 |
| GO:BP | response to peptide | 531 | 17 |
| GO:BP | cytoplasmic translational initiation | 35 | 4 |
| GO:BP | cellular response to peptide hormone stimulus | 309 | 12 |
| GO:BP | cellular response to vascular endothelial growth factor stimulus | 60 | 5 |
| GO:BP | rRNA-containing ribonucleoprotein complex export from nucleus | 17 | 3 |
| GO:BP | glutamine family amino acid biosynthetic process | 17 | 3 |
| GO:BP | translational initiation | 121 | 7 |
| GO:BP | secondary metabolic process | 61 | 5 |
| GO:BP | cellular amino acid biosynthetic process | 62 | 5 |
| GO:BP | body fluid secretion | 123 | 7 |
| GO:BP | ncRNA metabolic process | 449 | 15 |
| GO:BP | alpha-amino acid biosynthetic process | 62 | 5 |
| GO:BP | iron ion transport | 63 | 5 |
| GO:BP | activation of membrane attack complex | 5 | 2 |
| GO:BP | protein sulfation | 5 | 2 |
| GO:BP | viral translational termination-reinitiation | 5 | 2 |
| GO:BP | removal of superoxide radicals | 18 | 3 |
| GO:BP | arginine biosynthetic process | 5 | 2 |
| GO:BP | fatty acid beta-oxidation using acyl-CoA oxidase | 5 | 2 |
| GO:CC | cytoplasm | 11093 | 240 |
| GO:CC | intracellular anatomical structure | 14111 | 260 |
| GO:CC | cytosolic ribosome | 112 | 19 |
| GO:CC | ribosome | 236 | 25 |
| GO:CC | cytosol | 3849 | 110 |
| GO:CC | ribosomal subunit | 200 | 23 |
| GO:CC | intracellular organelle | 12510 | 232 |
| GO:CC | organelle | 12827 | 233 |
| GO:CC | small ribosomal subunit | 79 | 13 |
| GO:CC | intracellular membrane-bounded organelle | 11363 | 212 |
| GO:CC | cytosolic small ribosomal subunit | 45 | 10 |
| GO:CC | membrane-bounded organelle | 11812 | 213 |
| GO:CC | ribonucleoprotein complex | 725 | 32 |
| GO:CC | endomembrane system | 4006 | 95 |
| GO:CC | endoplasmic reticulum | 1761 | 53 |
| GO:CC | cytosolic large ribosomal subunit | 64 | 9 |
| GO:CC | organelle membrane | 3076 | 74 |
| GO:CC | mitochondrion | 1827 | 51 |
| GO:CC | large ribosomal subunit | 126 | 11 |
| GO:CC | organelle subcompartment | 1580 | 45 |
| GO:CC | polysomal ribosome | 32 | 6 |
| GO:CC | endoplasmic reticulum membrane | 993 | 31 |
| GO:CC | endoplasmic reticulum subcompartment | 999 | 31 |
| GO:CC | nuclear outer membrane-endoplasmic reticulum membrane network | 1018 | 31 |
| GO:CC | polysome | 70 | 7 |
| GO:CC | organelle envelope | 1176 | 32 |
| GO:CC | envelope | 1176 | 32 |
| GO:CC | mitochondrial envelope | 736 | 23 |
| GO:CC | chaperonin-containing T-complex | 10 | 3 |
| GO:CC | mitochondrial intermembrane space | 99 | 7 |
| GO:CC | rough endoplasmic reticulum | 105 | 7 |
| GO:CC | myelin sheath | 206 | 10 |
| GO:CC | organelle envelope lumen | 111 | 7 |
| GO:CC | eukaryotic 48S preinitiation complex | 15 | 3 |
| GO:CC | COP9 signalosome | 34 | 4 |
| GO:CC | eukaryotic translation initiation factor 3 complex | 16 | 3 |
| GO:CC | synapse | 1467 | 35 |
| GO:CC | eukaryotic 43S preinitiation complex | 17 | 3 |
| GO:CC | translation preinitiation complex | 18 | 3 |
| GO:CC | mitochondrial inner membrane | 451 | 15 |
| GO:CC | membrane-enclosed lumen | 4582 | 85 |
| GO:CC | organelle lumen | 4582 | 85 |
| GO:CC | intracellular organelle lumen | 4581 | 85 |
| GO:CC | cellular anatomical entity | 19567 | 286 |
| GO:CC | mitochondrial membrane | 677 | 19 |
| GO:CC | intracellular non-membrane-bounded organelle | 4500 | 83 |
| GO:CC | preribosome | 74 | 5 |
| GO:CC | non-membrane-bounded organelle | 4515 | 83 |
| GO:CC | preribosome, large subunit precursor | 24 | 3 |
| GO:CC | peroxisome | 148 | 7 |
| GO:CC | microbody | 148 | 7 |
| GO:MF | structural constituent of ribosome | 172 | 21 |
| GO:MF | oxidoreductase activity | 815 | 42 |
| GO:MF | rRNA binding | 69 | 12 |
| GO:MF | catalytic activity | 5665 | 128 |
| GO:MF | oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor | 143 | 13 |
| GO:MF | oxidoreductase activity, acting on CH-OH group of donors | 154 | 13 |
| GO:MF | flavin adenine dinucleotide binding | 90 | 10 |
| GO:MF | structural molecule activity | 612 | 25 |
| GO:MF | identical protein binding | 2140 | 54 |
| GO:MF | anion binding | 2420 | 58 |
| GO:MF | translation regulator activity | 145 | 10 |
| GO:MF | RNA binding | 1267 | 36 |
| GO:MF | oxidoreductase activity, acting on a sulfur group of donors | 51 | 6 |
| GO:MF | small molecule binding | 2543 | 59 |
| GO:MF | glutathione binding | 17 | 4 |
| GO:MF | oligopeptide binding | 17 | 4 |
| GO:MF | carbonyl reductase (NADPH) activity | 7 | 3 |
| GO:MF | NADP binding | 55 | 6 |
| GO:MF | lyase activity | 198 | 11 |
| GO:MF | enzyme inhibitor activity | 403 | 16 |
| GO:MF | ubiquitin ligase inhibitor activity | 9 | 3 |
| GO:MF | oxidoreductase activity, acting on the CH-CH group of donors | 60 | 6 |
| GO:MF | site-specific endodeoxyribonuclease activity, specific for altered base | 2 | 2 |
| GO:MF | N,N-dimethylaniline monooxygenase activity | 9 | 3 |
| GO:MF | amino acid binding | 63 | 6 |
| GO:MF | ubiquitin-protein transferase inhibitor activity | 10 | 3 |
| GO:MF | carboxylic ester hydrolase activity | 153 | 9 |
| GO:MF | mRNA 5’-UTR binding | 25 | 4 |
| GO:MF | ion binding | 5862 | 109 |
| GO:MF | palmitoyl-CoA oxidase activity | 3 | 2 |
| GO:MF | protein-disulfide reductase activity | 27 | 4 |
| GO:MF | transition metal ion binding | 1064 | 29 |
| GO:MF | 5.8S rRNA binding | 3 | 2 |
| GO:MF | carbon-sulfur lyase activity | 12 | 3 |
| GO:MF | nucleotide binding | 2185 | 49 |
| GO:MF | nucleoside phosphate binding | 2185 | 49 |
| GO:MF | acylglycerol lipase activity | 13 | 3 |
| GO:MF | 5S rRNA binding | 13 | 3 |
| GO:MF | steroid binding | 114 | 7 |
| GO:MF | translation regulator activity, nucleic acid binding | 113 | 7 |
| GO:MF | 3-hydroxy-arachidoyl-CoA dehydratase activity | 4 | 2 |
| GO:MF | glutathione transferase activity | 33 | 4 |
| GO:MF | 3-hydroxy-behenoyl-CoA dehydratase activity | 4 | 2 |
| GO:MF | 3-hydroxy-lignoceroyl-CoA dehydratase activity | 4 | 2 |
| GO:MF | very-long-chain 3-hydroxyacyl-CoA dehydratase activity | 4 | 2 |
| GO:MF | disulfide oxidoreductase activity | 34 | 4 |
| GO:MF | protein folding chaperone | 35 | 4 |
| GO:MF | NAD binding | 63 | 5 |
| GO:MF | oxidoreductase activity, acting on superoxide radicals as acceptor | 5 | 2 |
| GO:MF | stearoyl-CoA 9-desaturase activity | 5 | 2 |
| GO:MF | superoxide dismutase activity | 5 | 2 |
| GO:MF | lipase activity | 124 | 7 |
| GO:MF | organic cyclic compound binding | 5768 | 104 |
| GO:MF | FAD binding | 39 | 4 |
| GO:MF | transferase activity, transferring alkyl or aryl (other than methyl) groups | 65 | 5 |
| GO:MF | translation factor activity, RNA binding | 96 | 6 |
| GO:MF | complement binding | 20 | 3 |
| GO:MF | acyl-CoA oxidase activity | 6 | 2 |
| GO:MF | iron-sulfur cluster binding | 71 | 5 |
| GO:MF | metal cluster binding | 71 | 5 |
| GO:MF | metalloaminopeptidase activity | 22 | 3 |
| GO:MF | protein homodimerization activity | 676 | 19 |
| GO:MF | sulfur compound binding | 256 | 10 |
| GO:MF | ubiquitin-protein transferase regulator activity | 22 | 3 |
| HP | Abnormality of metabolism/homeostasis | 2240 | 65 |
| HP | Abnormal mean corpuscular volume | 45 | 6 |
| HP | Abnormal erythrocyte enzyme level | 26 | 5 |
| HP | Visceromegaly | 656 | 26 |
| HP | Reticulocytopenia | 29 | 5 |
| HP | Abnormal circulating metabolite concentration | 1099 | 37 |
| HP | Adenocarcinoma of the large intestine | 26 | 5 |
| HP | Abnormal erythrocyte morphology | 593 | 24 |
| HP | Abnormal enzyme/coenzyme activity | 477 | 22 |
| HP | Persistence of hemoglobin F | 25 | 5 |
| HP | Normochromic anemia | 29 | 5 |
| HP | Abnormal circulating glutamine concentration | 8 | 3 |
| HP | Abnormal hemoglobin | 49 | 6 |
| HP | Duplication of thumb phalanx | 49 | 6 |
| HP | Radial artery aplasia | 18 | 4 |
| HP | Elevated red cell adenosine deaminase level | 18 | 4 |
| HP | Hepatomegaly | 504 | 21 |
| HP | Abnormal radial artery morphology | 18 | 4 |
| HP | Adenocarcinoma of the intestines | 31 | 5 |
| HP | Partial duplication of thumb phalanx | 33 | 5 |
| KEGG | Ribosome | 169 | 21 |
| KEGG | Coronavirus disease - COVID-19 | 241 | 22 |
| KEGG | Metabolic pathways | 1563 | 63 |
| KEGG | Biosynthesis of unsaturated fatty acids | 34 | 7 |
| KEGG | Fatty acid elongation | 29 | 6 |
| KEGG | Drug metabolism - other enzymes | 92 | 9 |
| KEGG | Drug metabolism - cytochrome P450 | 71 | 8 |
| KEGG | Metabolism of xenobiotics by cytochrome P450 | 73 | 8 |
| KEGG | Biosynthesis of amino acids | 78 | 8 |
| KEGG | Glutathione metabolism | 71 | 7 |
| KEGG | Chemical carcinogenesis | 101 | 8 |
| KEGG | Biosynthesis of cofactors | 154 | 10 |
| KEGG | Fatty acid metabolism | 62 | 6 |
| REAC | Formation of a pool of free 40S subunits | 98 | 20 |
| REAC | L13a-mediated translational silencing of Ceruloplasmin expression | 108 | 20 |
| REAC | GTP hydrolysis and joining of the 60S ribosomal subunit | 109 | 20 |
| REAC | Metabolism | 1679 | 80 |
| REAC | Eukaryotic Translation Initiation | 116 | 20 |
| REAC | Cap-dependent Translation Initiation | 116 | 20 |
| REAC | SRP-dependent cotranslational protein targeting to membrane | 89 | 17 |
| REAC | Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) | 91 | 17 |
| REAC | Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) | 110 | 17 |
| REAC | Nonsense-Mediated Decay (NMD) | 110 | 17 |
| REAC | Translation | 217 | 23 |
| REAC | Formation of the ternary complex, and subsequently, the 43S complex | 49 | 12 |
| REAC | Ribosomal scanning and start codon recognition | 56 | 12 |
| REAC | Translation initiation complex formation | 56 | 12 |
| REAC | Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S | 57 | 12 |
| REAC | Major pathway of rRNA processing in the nucleolus and cytosol | 167 | 18 |
| REAC | rRNA processing | 167 | 18 |
| REAC | rRNA processing in the nucleus and cytosol | 167 | 18 |
| REAC | Biological oxidations | 204 | 17 |
| REAC | FMO oxidises nucleophiles | 3 | 3 |
| REAC | Phase II - Conjugation of compounds | 91 | 10 |
| REAC | Metabolism of lipids | 573 | 28 |
| REAC | Glutathione conjugation | 34 | 6 |
| REAC | Fatty acid metabolism | 169 | 12 |
| REAC | Formation of the active cofactor, UDP-glucuronate | 3 | 2 |
| REAC | alpha-linolenic (omega3) and linoleic (omega6) acid metabolism | 12 | 3 |
| REAC | alpha-linolenic acid (ALA) metabolism | 12 | 3 |
| TF | Factor: Kaiso; motif: SARNYCTCGCGAGAN; match class: 1 | 9949 | 200 |
| TF | Factor: E2F-1; motif: GNGGGCGGGRMN | 14228 | 252 |
| TF | Factor: ZF5; motif: GSGCGCGR | 14821 | 257 |
| TF | Factor: FOXN4; motif: NNWANNCGWMCGCGTCNNNNMT; match class: 1 | 12768 | 232 |
| TF | Factor: AhR; motif: NTNGCGTGNNN | 3488 | 93 |
| TF | Factor: FOXN4; motif: NNWANNCGWMCGCGTCNNNNMT | 16009 | 268 |
| TF | Factor: E2F-4; motif: NTTTCSCGCC | 10545 | 201 |
| TF | Factor: ELK-1; motif: ACCGGAWRTN | 14697 | 253 |
| TF | Factor: LKLF; motif: NGGGCGG | 7220 | 152 |
| TF | Factor: CPBP; motif: NGGGCGG | 7220 | 152 |
| TF | Factor: Sp3; motif: AGGGCGG | 7220 | 152 |
| TF | Factor: SP6; motif: WGGGCGG | 7220 | 152 |
| TF | Factor: ZF5; motif: NRNGNGCGCGCWN | 14469 | 249 |
| TF | Factor: E2F; motif: GGCGSG | 10391 | 195 |
| TF | Factor: ZF5; motif: NRNGNGCGCGCWN; match class: 1 | 11181 | 205 |
| TF | Factor: ZF5; motif: GSGCGCGR; match class: 1 | 12032 | 215 |
| TF | Factor: BEN; motif: CAGCGRNV; match class: 1 | 11980 | 214 |
| TF | Factor: AhR:Arnt; motif: KNNKNNTYGCGTGCMS | 2875 | 76 |
| TF | Factor: Kaiso; motif: SARNYCTCGCGAGAN | 13491 | 233 |
| TF | Factor: E2F-1; motif: GNGGGCGGGRMN; match class: 1 | 10601 | 195 |
| TF | Factor: Hes1; motif: NNCACGYGNN; match class: 1 | 11386 | 205 |
| TF | Factor: Elk-1; motif: NNNNCCGGAARTNN | 10072 | 187 |
| TF | Factor: E2F-1; motif: NNNSSCGCSAANN | 9013 | 172 |
| TF | Factor: Klf17; motif: NGGGCGG | 6533 | 135 |
| TF | Factor: Hes1; motif: NNCACGYGNN | 15504 | 255 |
| TF | Factor: AhR,; motif: NRCGTGNGN | 4421 | 100 |
| TF | Factor: PEA3; motif: RCCGGAAGYN | 9964 | 183 |
| TF | Factor: ZF5; motif: GYCGCGCARNGCNN | 9484 | 176 |
| TF | Factor: AhR; motif: CCYCNRRSTNGCGTGASA | 3480 | 82 |
| TF | Factor: E2F-4; motif: GNNGGCGGGAAN | 5907 | 120 |
| TF | Factor: SP100; motif: NNCGTCGNNTAAWNN | 8478 | 158 |
| TF | Factor: E2F; motif: NCSCGCSAAAN | 5198 | 108 |
| TF | Factor: IRF6; motif: NNNACTCYCGGKNNN | 13409 | 224 |
| TF | Factor: GABP-alpha; motif: CTTCCK | 10764 | 189 |
| TF | Factor: AHR; motif: CACGCN; match class: 1 | 2729 | 66 |
| TF | Factor: E2F-7; motif: GRGGCGGGAANNN | 7914 | 148 |
| TF | Factor: MYF6; motif: NNNRACAGNCNCNCC; match class: 1 | 7012 | 134 |
| TF | Factor: E2F; motif: TTTSGCGSG | 5455 | 110 |
| TF | Factor: ELK-1; motif: ACCGGAWRTN; match class: 1 | 9029 | 163 |
| TF | Factor: LKLF; motif: NGGGCGG; match class: 1 | 2360 | 58 |
| TF | Factor: Sp3; motif: AGGGCGG; match class: 1 | 2360 | 58 |
| TF | Factor: SP6; motif: WGGGCGG; match class: 1 | 2360 | 58 |
| TF | Factor: CPBP; motif: NGGGCGG; match class: 1 | 2360 | 58 |
| TF | Factor: E2F1; motif: NNNNNGCGSSAAAN | 5835 | 115 |
| TF | Factor: E2F-3; motif: GGCGGGN | 11268 | 193 |
| TF | Factor: ZF5; motif: GYCGCGCARNGCNN; match class: 1 | 5819 | 114 |
| TF | Factor: TEL1; motif: CNCGGAANNN | 10420 | 181 |
| TF | Factor: MYF6; motif: NNNRACAGNCNCNCC | 14294 | 232 |
| TF | Factor: BEN; motif: CWGCGAYA | 6569 | 125 |
| TF | Factor: IRF4; motif: NNNAYTCTCGGWNNN; match class: 1 | 8126 | 148 |
| TF | Factor: AhR:Arnt; motif: GRGKATYGCGTGMCWNSCC | 5815 | 113 |
| TF | Factor: Egr-2; motif: GCGTGGGCGG | 7210 | 134 |
| TF | Factor: AhR; motif: NTNGCGTGNNN; match class: 1 | 393 | 17 |
| TF | Factor: E2F-1; motif: TTTSGCGS | 5974 | 115 |
| TF | Factor: BEN; motif: CAGCGRNV | 16234 | 255 |
| TF | Factor: Pax-5; motif: RRMSWGANWYCTNRAGCGKRACSRYNSM | 11986 | 201 |
| TF | Factor: c-Myc:Max; motif: GCCAYGYGSN; match class: 1 | 2409 | 57 |
| TF | Factor: p53; motif: RGRCWWGYCYNGRCWWGYYY | 7799 | 142 |
| TF | Factor: Pax-3; motif: NNNNNNCGTCACGSTYNNNNN | 12917 | 213 |
| TF | Factor: E2F-1; motif: NTTSGCGG; match class: 1 | 1815 | 46 |
| TF | Factor: RNF96; motif: BCCCGCRGCC | 6337 | 120 |
| TF | Factor: ERG; motif: ACCGGAART | 9550 | 166 |
| TF | Factor: HES-1; motif: GSCACGMGMC | 3590 | 76 |
| TF | Factor: ZBED6; motif: NRRGCTCGCCNN | 5544 | 107 |
| TF | Factor: AhR; motif: NNNKNGCGTGNSNNNNN | 1222 | 34 |
| TF | Factor: SP4; motif: NNWAGGCGTGNCNNN | 4923 | 97 |
| TF | Factor: Pax-5; motif: RRMSWGANWYCTNRAGCGKRACSRYNSM; match class: 1 | 5518 | 106 |
| TF | Factor: TEL1; motif: CNCGGAANNN; match class: 1 | 4384 | 88 |
| TF | Factor: E2F-1; motif: TTTSGCGCGMNR | 5994 | 113 |
| TF | Factor: SP4; motif: NNKGGGCGKGNCN | 1941 | 47 |
| TF | Factor: E2F; motif: NNTTTCGCGCN | 5159 | 100 |
| TF | Factor: SP1:SP3; motif: CCSCCCCCYCC | 6684 | 123 |
| TF | Factor: E2F; motif: NKCGCGCSAAAN | 4858 | 95 |
| TF | Factor: Ets2; motif: ACCGGAWRYN | 7919 | 141 |
| TF | Factor: E2F-4; motif: GCGGGAAANA | 10318 | 175 |
| TF | Factor: NGFI-C; motif: WTGCGTGGGYGG | 5000 | 97 |
| TF | Factor: BCL6B; motif: NNNNCCGCCCCWNNNN | 13664 | 220 |
| TF | Factor: HIF-1alpha; motif: NCACGT | 6382 | 118 |
| TF | Factor: CTCF; motif: NAGGGGGCGCNNKNNNN; match class: 1 | 9341 | 161 |
| TF | Factor: Tcfl5; motif: NNCNCGNGNN | 6337 | 117 |
| TF | Factor: EGR-1; motif: TGCGTGGGCGK | 4136 | 83 |
| TF | Factor: HIC1; motif: NNNGGKTGCCCSNNNNNN | 2851 | 62 |
| TF | Factor: IRF4; motif: NNNAYTCTCGGWNNN | 14544 | 231 |
| TF | Factor: Tcfl5; motif: NNCNCGNGNN; match class: 1 | 6337 | 117 |
| TF | Factor: c-ets-1; motif: ACCGGAWRYN | 8408 | 147 |
| TF | Factor: E2F-4; motif: NGGGGGCGGGRMNN | 6987 | 126 |
| TF | Factor: Egr-3; motif: NTGCGTGGGCGK | 6055 | 112 |
| TF | Factor: AhR; motif: CCYCNRRSTNGCGTGASA; match class: 1 | 383 | 15 |
| TF | Factor: E2F-1; motif: TTTSGCGS; match class: 1 | 1582 | 39 |
| TF | Factor: arnt; motif: CACGYA | 4582 | 89 |
| TF | Factor: HIF-1alpha; motif: GNACGTGM | 6619 | 120 |
| TF | Factor: Zic1; motif: NNCCCCCGGGGGGG | 9522 | 162 |
| TF | Factor: SP2; motif: GGGCGGGAC; match class: 1 | 3289 | 68 |
| TF | Factor: Elf-1; motif: AWCCCGGAAGTN | 8375 | 145 |
| TF | Factor: E2F-1; motif: NNNSSCGCSAANN; match class: 1 | 4125 | 81 |
| TF | Factor: SP2; motif: GGGCGGGAC | 8107 | 141 |
| TF | Factor: c-Ets-1; motif: NNNRCCGGAWRYNNNN | 7309 | 129 |
| TF | Factor: Sp1; motif: GGNGGGGGNGGGGGMGGGGCNGGG | 10752 | 178 |
| TF | Factor: ELF4; motif: CCCGGAARTN | 7185 | 127 |
| TF | Factor: AP-2alpha; motif: NGCCYSNNGSN | 6174 | 112 |
| TF | Factor: ZBED6; motif: NRRGCTCGCCNN; match class: 1 | 1364 | 34 |
| TF | Factor: Kid3; motif: CCACN; match class: 1 | 21165 | 303 |
| TF | Factor: Erm; motif: NCCGGAWGTN | 5268 | 98 |
| TF | Factor: AP-2; motif: MKCCCSCNGGCG | 8029 | 139 |
| TF | Factor: SP100; motif: NNCGTCGNNTAAWNN; match class: 1 | 3060 | 63 |
| TF | Factor: HES-1; motif: NNCKYGTGNNN | 4062 | 79 |
| TF | Factor: CPBP; motif: SNCCCNN; match class: 1 | 19929 | 292 |
| TF | Factor: AP-2; motif: SNNNCCNCAGGCN | 7085 | 125 |
| TF | Factor: E2F-4; motif: GCGGGAAANA; match class: 1 | 4700 | 89 |
| TF | Factor: GKLF; motif: GCCMCRCCCNNN | 7840 | 136 |
| TF | Factor: Egr-2; motif: NTGCGTRGGCGK | 5359 | 99 |
| TF | Factor: AP-2beta; motif: GCNNNGGSCNGVGGGN | 5101 | 95 |
| TF | Factor: E2F-4; motif: NTTTCSCGCC; match class: 1 | 5364 | 99 |
| TF | Factor: GKLF; motif: WGGGYGKGGCCN | 8978 | 152 |
| TF | Factor: Sp1; motif: NGGGGCGGGGN | 9122 | 154 |
| TF | Factor: GKLF; motif: WGGGYGKGGCCN; match class: 1 | 3595 | 71 |
| TF | Factor: c-Myc:Max; motif: GCCAYGYGSN | 7338 | 128 |
| TF | Factor: MAF; motif: GCTGAGTCAN | 6937 | 122 |
| TF | Factor: GKLF; motif: NNNRGGNGNGGSN | 15302 | 237 |
| TF | Factor: E2F-3; motif: GGCGGGN; match class: 1 | 6875 | 121 |
| TF | Factor: AHR; motif: CACGCN | 8469 | 144 |
| TF | Factor: Zscan2; motif: GTCAAAACGC | 59 | 5 |
| TF | Factor: WT1; motif: SMCNCCNSC | 8128 | 139 |
| TF | Factor: AP-2gamma; motif: GCCYNCRGSN | 7106 | 124 |
| TF | Factor: ER71; motif: ACCGGAARYN | 4325 | 82 |
| TF | Factor: SAP-1a; motif: NRRCCGGAAGYRN | 9134 | 153 |
| TF | Factor: Egr-2; motif: GCGTGGGCGG; match class: 1 | 2774 | 57 |
| TF | Factor: Pax-3; motif: NNNNNNCGTCACGSTYNNNNN; match class: 1 | 6178 | 110 |
| TF | Factor: ctcf; motif: CCNCNAGRKGGCRSTN | 5575 | 101 |
| TF | Factor: Kaiso; motif: GCMGGGRGCRGS | 11131 | 181 |
| TF | Factor: BTEB2; motif: RGGGNGKGGN | 7600 | 131 |
| TF | Factor: IRF6; motif: NNNACTCYCGGKNNN; match class: 1 | 7128 | 124 |
| TF | Factor: GABPalpha_GABPbeta; motif: CTTCCKGY | 2969 | 60 |
| TF | Factor: E2F; motif: TTTSGCGSG | 4808 | 89 |
| TF | Factor: E2F-1; motif: NKTSSCGC | 7904 | 135 |
| TF | Factor: E2F-1; motif: NKTSSCGC; match class: 1 | 2922 | 59 |
| TF | Factor: Pet-1; motif: GCNGGAAGYG | 13321 | 210 |
| TF | Factor: LRH-1; motif: NYCAAGGYCAN; match class: 1 | 411 | 14 |
| TF | Factor: CTCF; motif: NAGGGGGCGCNNKNNNN | 14310 | 223 |
| TF | Factor: WT1; motif: NGCGGGGGGGTSMMCYN | 5297 | 96 |
| WP | Cytoplasmic Ribosomal Proteins | 81 | 17 |
| WP | Omega-3/Omega-6 FA synthesis | 15 | 4 |
| WP | Metapathway biotransformation | 141 | 11 |
| WP | Translation Factors | 49 | 6 |
| WP | Selenium Micronutrient Network | 23 | 4 |
| WP | Folic Acid Network | 23 | 4 |
| WP | Oxidative Stress and Redox Pathway | 93 | 8 |
2.2.14 Functional Enrichment - Kidney-specific TCDD-AhR Regulated
kable(Diff_Kidney_Interx_PathwayEnrichment$result %>% dplyr::select(source, term_name, term_size, intersection_size),
table.attr = "class=\"striped\"", format = "html")| source | term_name | term_size | intersection_size |
|---|---|---|---|
| GO:BP | cellular response to decreased oxygen levels | 156 | 3 |
| GO:BP | cellular response to oxygen levels | 175 | 3 |
| GO:BP | cellular response to hypoxia | 146 | 3 |
| GO:BP | regulation of B cell differentiation | 30 | 2 |
| GO:BP | regulation of Wnt signaling pathway involved in dorsal/ventral axis specification | 2 | 1 |
| GO:BP | epithelial cell proliferation | 424 | 3 |
| GO:BP | reproductive structure development | 503 | 3 |
| GO:BP | regulation of fibroblast proliferation | 102 | 2 |
| GO:BP | negative regulation of canonical Wnt signaling pathway involved in controlling type B pancreatic cell proliferation | 1 | 1 |
| GO:BP | negative regulation of myeloid cell differentiation | 97 | 2 |
| GO:BP | positive regulation of fat cell differentiation | 67 | 2 |
| GO:BP | negative regulation of B cell differentiation | 3 | 1 |
| GO:BP | stromal-epithelial cell signaling involved in prostate gland development | 1 | 1 |
| GO:BP | cellular response to fibroblast growth factor stimulus | 97 | 2 |
| GO:BP | canonical Wnt signaling pathway involved in regulation of type B pancreatic cell proliferation | 2 | 1 |
| GO:BP | Wnt signaling pathway involved in dorsal/ventral axis specification | 2 | 1 |
| GO:BP | cellular catabolic process | 2059 | 5 |
| GO:BP | GDP-L-fucose salvage | 1 | 1 |
| GO:BP | GDP-L-fucose biosynthetic process | 3 | 1 |
| GO:BP | epidermal growth factor receptor signaling pathway via MAPK cascade | 1 | 1 |
| GO:BP | response to decreased oxygen levels | 341 | 3 |
| GO:BP | tube development | 1137 | 4 |
| GO:BP | tube morphogenesis | 911 | 4 |
| GO:BP | regulation of epithelial cell proliferation | 359 | 3 |
| GO:BP | negative regulation of Wnt signaling pathway involved in dorsal/ventral axis specification | 2 | 1 |
| GO:BP | reproductive system development | 508 | 3 |
| GO:BP | response to oxygen levels | 368 | 3 |
| GO:BP | negative regulation of planar cell polarity pathway involved in axis elongation | 2 | 1 |
| GO:BP | regulation of planar cell polarity pathway involved in axis elongation | 2 | 1 |
| GO:BP | positive regulation of aggrephagy | 3 | 1 |
| GO:BP | regulation of aggrephagy | 3 | 1 |
| GO:BP | regulation of morphogenesis of an epithelium | 69 | 2 |
| GO:BP | positive regulation of intracellular mRNA localization | 3 | 1 |
| GO:BP | regulation of intracellular mRNA localization | 3 | 1 |
| GO:BP | phytanic acid metabolic process | 1 | 1 |
| GO:BP | response to raffinose | 1 | 1 |
| GO:BP | ERK1 and ERK2 cascade | 344 | 3 |
| GO:BP | cellular response to raffinose | 1 | 1 |
| GO:BP | positive regulation of canonical Wnt signaling pathway | 106 | 2 |
| GO:BP | convergent extension involved in somitogenesis | 1 | 1 |
| GO:BP | Wnt signaling pathway involved in somitogenesis | 3 | 1 |
| GO:BP | circulatory system development | 1174 | 4 |
| GO:BP | monocarboxylic acid catabolic process | 122 | 2 |
| GO:BP | response to fibroblast growth factor | 104 | 2 |
| GO:BP | lipid oxidation | 120 | 2 |
| GO:BP | regulation of canonical Wnt signaling pathway involved in controlling type B pancreatic cell proliferation | 2 | 1 |
| GO:BP | cellular response to interleukin-1 | 103 | 2 |
| GO:BP | methyl-branched fatty acid metabolic process | 3 | 1 |
| GO:BP | positive regulation of cellular catabolic process | 414 | 3 |
| GO:BP | fibroblast proliferation | 104 | 2 |
| GO:BP | response to organic cyclic compound | 1043 | 4 |
| GO:BP | septum transversum development | 2 | 1 |
| GO:BP | positive regulation of catabolic process | 481 | 3 |
| GO:BP | proepicardium development | 2 | 1 |
| GO:BP | response to abiotic stimulus | 1177 | 4 |
| GO:BP | response to hypoxia | 326 | 3 |
| GO:BP | fatty acid metabolic process | 425 | 3 |
| GO:BP | MAPK cascade | 771 | 4 |
| GO:BP | regulation of myeloid leukocyte differentiation | 125 | 2 |
| GO:BP | neural crest cell fate commitment | 3 | 1 |
| GO:BP | fatty acid catabolic process | 99 | 2 |
| GO:BP | fatty acid oxidation | 114 | 2 |
| GO:BP | phosphatidylinositol 3-kinase signaling | 127 | 2 |
| GO:BP | response to interleukin-1 | 131 | 2 |
| GO:BP | positive regulation of Wnt signaling pathway | 136 | 2 |
| GO:BP | cellular response to heparin | 4 | 1 |
| GO:BP | GDP-L-fucose metabolic process | 4 | 1 |
| GO:BP | axis elongation involved in somitogenesis | 4 | 1 |
| GO:BP | regulation of fat cell differentiation | 142 | 2 |
| GO:BP | canonical Wnt signaling pathway involved in regulation of cell proliferation | 5 | 1 |
| GO:BP | positive regulation of hyaluronan biosynthetic process | 5 | 1 |
| GO:BP | regulation of midbrain dopaminergic neuron differentiation | 5 | 1 |
| GO:BP | response to organic substance | 3418 | 6 |
| GO:BP | regulation of cell cycle process | 599 | 3 |
| GO:BP | stem cell fate commitment | 5 | 1 |
| GO:BP | nuclear-transcribed mRNA catabolic process, deadenylation-independent decay | 5 | 1 |
| GO:BP | epithelial tube formation | 151 | 2 |
| GO:BP | B cell differentiation | 147 | 2 |
| GO:BP | response to heparin | 5 | 1 |
| GO:BP | planar cell polarity pathway involved in axis elongation | 5 | 1 |
| GO:BP | fatty acid beta-oxidation using acyl-CoA oxidase | 5 | 1 |
| GO:BP | tube formation | 163 | 2 |
| GO:BP | phosphatidylinositol-mediated signaling | 162 | 2 |
| GO:BP | monocarboxylic acid metabolic process | 616 | 3 |
| GO:BP | inositol lipid-mediated signaling | 165 | 2 |
| GO:BP | prostate glandular acinus morphogenesis | 6 | 1 |
| GO:BP | regulation of branching involved in prostate gland morphogenesis | 6 | 1 |
| GO:BP | prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis | 6 | 1 |
| GO:BP | negative regulation of non-canonical Wnt signaling pathway | 6 | 1 |
| GO:BP | placenta development | 172 | 2 |
| GO:BP | catabolic process | 2399 | 5 |
| GO:BP | blood vessel morphogenesis | 647 | 3 |
| GO:BP | positive regulation of developmental process | 1412 | 4 |
| GO:BP | regulation of lymphocyte differentiation | 178 | 2 |
| GO:BP | neural tube development | 181 | 2 |
| GO:BP | regulation of keratinocyte apoptotic process | 7 | 1 |
| GO:BP | regulation of multicellular organismal development | 1444 | 4 |
| GO:BP | fatty acid alpha-oxidation | 7 | 1 |
| GO:BP | keratinocyte apoptotic process | 7 | 1 |
| GO:BP | chorio-allantoic fusion | 8 | 1 |
| GO:BP | positive regulation of signal transduction | 1506 | 4 |
| GO:BP | regulation of MAPK cascade | 708 | 3 |
| GO:BP | positive regulation of epithelial tube formation | 8 | 1 |
| GO:BP | regulation of epithelial tube formation | 8 | 1 |
| GO:BP | regulation of dopaminergic neuron differentiation | 8 | 1 |
| GO:BP | aggrephagy | 8 | 1 |
| GO:BP | convergent extension involved in axis elongation | 8 | 1 |
| GO:BP | cellular response to tumor necrosis factor | 198 | 2 |
| GO:BP | negative regulation of fibroblast apoptotic process | 10 | 1 |
| GO:BP | negative regulation of secretion | 207 | 2 |
| GO:BP | carboxylic acid catabolic process | 221 | 2 |
| GO:BP | convergent extension involved in gastrulation | 10 | 1 |
| GO:BP | cellular response to steroid hormone stimulus | 205 | 2 |
| GO:BP | positive regulation of fibroblast apoptotic process | 9 | 1 |
| GO:BP | brain development | 758 | 3 |
| GO:BP | myeloid leukocyte differentiation | 219 | 2 |
| GO:BP | lipid modification | 218 | 2 |
| GO:BP | positive regulation of epithelial cell proliferation | 205 | 2 |
| GO:BP | regulation of cellular catabolic process | 745 | 3 |
| GO:BP | positive regulation of monocyte differentiation | 10 | 1 |
| GO:BP | positive regulation of protein localization to early endosome | 9 | 1 |
| GO:BP | regulation of protein localization to early endosome | 9 | 1 |
| GO:BP | protein kinase B signaling | 214 | 2 |
| GO:BP | cellular lipid catabolic process | 214 | 2 |
| GO:BP | blood vessel development | 743 | 3 |
| GO:BP | regulation of hyaluronan biosynthetic process | 9 | 1 |
| GO:BP | positive regulation of execution phase of apoptosis | 10 | 1 |
| GO:BP | positive regulation of peroxisome proliferator activated receptor signaling pathway | 9 | 1 |
| GO:BP | morphogenesis of a branching structure | 220 | 2 |
| GO:BP | morphogenesis of a branching epithelium | 203 | 2 |
| GO:BP | response to tumor necrosis factor | 223 | 2 |
| GO:BP | regulation of myeloid cell differentiation | 217 | 2 |
| GO:BP | positive regulation of cerebellar granule cell precursor proliferation | 11 | 1 |
| GO:BP | vasculature development | 773 | 3 |
| GO:BP | positive regulation of ERK1 and ERK2 cascade | 225 | 2 |
| GO:BP | protein localization to early endosome | 11 | 1 |
| GO:BP | prostate glandular acinus development | 11 | 1 |
| GO:BP | bone trabecula formation | 11 | 1 |
| GO:BP | organic acid catabolic process | 228 | 2 |
| GO:BP | neural crest formation | 11 | 1 |
| GO:BP | dorsal/ventral axis specification | 11 | 1 |
| GO:BP | negative regulation of erythrocyte differentiation | 11 | 1 |
| GO:BP | cellular response to transforming growth factor beta stimulus | 231 | 2 |
| GO:BP | response to transforming growth factor beta | 235 | 2 |
| GO:BP | mesendoderm development | 11 | 1 |
| GO:BP | stress-activated MAPK cascade | 231 | 2 |
| GO:BP | positive regulation of extrinsic apoptotic signaling pathway via death domain receptors | 13 | 1 |
| GO:BP | midbrain dopaminergic neuron differentiation | 14 | 1 |
| GO:BP | cellular response to cytokine stimulus | 822 | 3 |
| GO:BP | positive regulation of protein localization to endosome | 13 | 1 |
| GO:BP | cellular response to X-ray | 12 | 1 |
| GO:BP | regulation of Wnt signaling pathway, planar cell polarity pathway | 14 | 1 |
| GO:BP | intracellular mRNA localization | 12 | 1 |
| GO:BP | regulation of protein localization to endosome | 14 | 1 |
| GO:BP | planar cell polarity pathway involved in neural tube closure | 12 | 1 |
| GO:BP | regulation of establishment of planar polarity involved in neural tube closure | 13 | 1 |
| GO:BP | bone trabecula morphogenesis | 14 | 1 |
| GO:BP | regulation of type B pancreatic cell proliferation | 14 | 1 |
| GO:BP | establishment of planar polarity involved in neural tube closure | 14 | 1 |
| GO:BP | positive regulation of non-canonical Wnt signaling pathway | 14 | 1 |
| GO:BP | cellular response to salt stress | 14 | 1 |
| GO:BP | regulation of cerebellar granule cell precursor proliferation | 14 | 1 |
| GO:BP | negative regulation of platelet-derived growth factor receptor signaling pathway | 13 | 1 |
| GO:BP | stress-activated protein kinase signaling cascade | 246 | 2 |
| GO:BP | intracellular receptor signaling pathway | 244 | 2 |
| GO:BP | head development | 805 | 3 |
| GO:BP | regulation of B cell activation | 248 | 2 |
| GO:BP | branching involved in prostate gland morphogenesis | 13 | 1 |
| GO:BP | hyaluronan biosynthetic process | 14 | 1 |
| GO:BP | nucleotide salvage | 14 | 1 |
| GO:BP | small molecule metabolic process | 1713 | 4 |
| GO:BP | positive regulation of cell communication | 1725 | 4 |
| GO:BP | fat cell differentiation | 247 | 2 |
| GO:BP | cellular potassium ion homeostasis | 13 | 1 |
| GO:BP | positive regulation of signaling | 1732 | 4 |
| GO:BP | establishment or maintenance of transmembrane electrochemical gradient | 12 | 1 |
| GO:BP | regulation of canonical Wnt signaling pathway | 241 | 2 |
| GO:BP | positive regulation of epidermal growth factor-activated receptor activity | 13 | 1 |
| GO:BP | sodium ion export across plasma membrane | 14 | 1 |
| GO:BP | regulation of cell population proliferation | 1753 | 4 |
| GO:BP | regulation of cellular localization | 867 | 3 |
| GO:BP | regulation of peptidyl-tyrosine phosphorylation | 267 | 2 |
| GO:BP | establishment of planar polarity of embryonic epithelium | 16 | 1 |
| GO:BP | carboxylic acid metabolic process | 896 | 3 |
| GO:BP | oxoacid metabolic process | 908 | 3 |
| GO:BP | negative regulation of JUN kinase activity | 15 | 1 |
| GO:BP | mesenchyme development | 280 | 2 |
| GO:BP | negative regulation of osteoblast proliferation | 16 | 1 |
| GO:BP | positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay | 16 | 1 |
| GO:BP | convergent extension | 16 | 1 |
| GO:BP | 3’-UTR-mediated mRNA destabilization | 16 | 1 |
| GO:BP | export from cell | 908 | 3 |
| GO:BP | regulation of cell cycle | 898 | 3 |
| GO:BP | cellular response to prostaglandin E stimulus | 15 | 1 |
| GO:BP | cellular response to stress | 1805 | 4 |
| GO:BP | regulation of peroxisome proliferator activated receptor signaling pathway | 16 | 1 |
| GO:BP | nucleotide-sugar biosynthetic process | 16 | 1 |
| GO:BP | regulation of catabolic process | 893 | 3 |
| GO:BP | regulation of protein secretion | 292 | 2 |
| GO:BP | regulation of MAP kinase activity | 288 | 2 |
| GO:BP | regulation of leukocyte differentiation | 292 | 2 |
| GO:BP | negative regulation of androgen receptor signaling pathway | 17 | 1 |
| GO:BP | regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay | 17 | 1 |
| GO:BP | enzyme linked receptor protein signaling pathway | 916 | 3 |
| GO:BP | negative regulation of cholesterol efflux | 17 | 1 |
| GO:BP | canonical Wnt signaling pathway | 290 | 2 |
| GO:BP | negative regulation of cell migration | 289 | 2 |
| GO:BP | cell migration involved in heart development | 17 | 1 |
| GO:BP | regulation of monocyte differentiation | 18 | 1 |
| GO:BP | protein localization to peroxisome | 18 | 1 |
| GO:BP | negative regulation of nitric oxide biosynthetic process | 18 | 1 |
| GO:BP | spongiotrophoblast layer development | 18 | 1 |
| GO:BP | regulation of cell migration | 934 | 3 |
| GO:BP | response to cytokine | 935 | 3 |
| GO:BP | organic acid metabolic process | 944 | 3 |
| GO:BP | cellular response to estrogen stimulus | 18 | 1 |
| GO:BP | negative regulation of nitric oxide metabolic process | 18 | 1 |
| GO:BP | regulation of Wnt signaling pathway | 302 | 2 |
| GO:BP | protein targeting to peroxisome | 18 | 1 |
| GO:BP | establishment of protein localization to peroxisome | 18 | 1 |
| GO:BP | negative regulation of cell motility | 303 | 2 |
| GO:BP | cell proliferation in external granule layer | 19 | 1 |
| GO:BP | regulation of endocytic recycling | 19 | 1 |
| GO:BP | regulation of anatomical structure morphogenesis | 963 | 3 |
| GO:BP | regulation of execution phase of apoptosis | 19 | 1 |
| GO:BP | transport | 4502 | 6 |
| GO:BP | cerebellar granule cell precursor proliferation | 19 | 1 |
| GO:BP | cellular response to environmental stimulus | 313 | 2 |
| GO:BP | negative regulation of cellular component movement | 313 | 2 |
| GO:BP | cellular response to abiotic stimulus | 313 | 2 |
| GO:BP | tissue development | 1923 | 4 |
| GO:BP | cell proliferation in hindbrain | 20 | 1 |
| GO:BP | cellular response to prostaglandin stimulus | 20 | 1 |
| GO:BP | negative regulation of bone remodeling | 20 | 1 |
| GO:BP | regulation of cell motility | 986 | 3 |
| GO:BP | regulation of ERK1 and ERK2 cascade | 325 | 2 |
| GO:BP | mammary gland alveolus development | 21 | 1 |
| GO:BP | cellular sodium ion homeostasis | 21 | 1 |
| GO:BP | peroxisomal transport | 21 | 1 |
| GO:BP | cellular lipid metabolic process | 994 | 3 |
| GO:BP | mammary gland lobule development | 21 | 1 |
| GO:BP | peroxisome proliferator activated receptor signaling pathway | 22 | 1 |
| GO:BP | lipid catabolic process | 335 | 2 |
| GO:BP | regulation of fibroblast apoptotic process | 22 | 1 |
| GO:BP | nitrogen compound transport | 1986 | 4 |
| GO:BP | organic substance catabolic process | 1985 | 4 |
| GO:BP | cellular response to vitamin D | 22 | 1 |
| GO:BP | negative regulation of locomotion | 336 | 2 |
| GO:BP | central nervous system development | 1023 | 3 |
| GO:BP | establishment of localization | 4658 | 6 |
| GO:MF | prostaglandin-I synthase activity | 1 | 1 |
| GO:MF | pristanoyl-CoA oxidase activity | 1 | 1 |
| GO:MF | fucokinase activity | 1 | 1 |
| GO:MF | P-type potassium:proton transporter activity | 3 | 1 |
| GO:MF | thiamine pyrophosphate binding | 8 | 1 |
| GO:MF | lyase activity | 198 | 2 |
| GO:MF | oxidoreductase activity, acting on the CH-CH group of donors, oxygen as acceptor | 9 | 1 |
| GO:MF | P-type sodium transporter activity | 9 | 1 |
| GO:MF | P-type sodium:potassium-exchanging transporter activity | 9 | 1 |
| GO:MF | hydroperoxy icosatetraenoate dehydratase activity | 7 | 1 |
| GO:MF | acyl-CoA oxidase activity | 6 | 1 |
| REAC | Peroxisomal lipid metabolism | 27 | 2 |
| REAC | Fatty acid metabolism | 169 | 3 |
| REAC | Sterols are 12-hydroxylated by CYP8B1 | 1 | 1 |
| REAC | Peroxisomal protein import | 61 | 2 |
| WP | Eicosanoid metabolism via Cyclo Oxygenases (COX) | 31 | 2 |